Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xaj Working: n-1-141.cluster.ucsf.bkslab.org:/scratch/xiaobo/6899/xaj-8058088.10 Result: /scratch/xiaobo/6899/xaj-8058088.10 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaj 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/xab/inputs/xaj mkdir: created directory `/scratch/xiaobo/6899' mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10' /scratch/xiaobo/6899/xaj-8058088.10 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/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/6899/xaj-8058088.10/working' mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/protonate' Storing results in /scratch/xiaobo/6899/xaj-8058088.10/finished Working in /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 /scratch/xiaobo/6899/xaj-8058088.10/working/protonate /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Using inputs as protomers/tautomers. No processing done 456 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/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Bulk generating 3D conformations all protomers in /scratch/xiaobo/6899/xaj-8058088.10/working/3D mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/6899/xaj-8058088.10/working/protonate/xaj-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 ZINC001435610979 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building' mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435610979' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435610979 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001435610979 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435610979/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435610979 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/1 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cc(Cl)ccc1Br)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001435610979.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435610979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435610979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435610979 none O=C(NCCc1cc(Cl)ccc1Br)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 1, 17, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 12, 20, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 12, 12, 20, 20, 26, 26, 26, 6, 6, 6, 6, 6, 6, 6] 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, 39, 40]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435610979 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435610979 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/finished' Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435610979/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435610979 Building ZINC001435677501 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435677501 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/2 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1[C@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C) `ZINC001435677501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435677501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001435677501 none CO[C@@H]1[C@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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.3', 'F', 'F', 'F', '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, 12, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 9, 9, 9, 12, 12, 12, 9, 9, 9, 2, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 9, 9, 9, 9, 9, 9] 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, 54, 55, 56]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/3 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1[C@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C) `ZINC001435677501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435677501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001435677501 none CO[C@@H]1[C@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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.3', 'F', 'F', 'F', '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, 12, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 11, 11, 11, 15, 15, 15, 11, 11, 11, 2, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 11, 11, 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, 51, 52, 53, 54, 55, 56]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435677501 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501 Building ZINC001435677501 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435677501 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 2) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CO[C@@H]1[C@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C) `ZINC001435677501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435677501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001435677501 none CO[C@@H]1[C@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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.3', 'F', 'F', 'F', '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, 12, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 9, 9, 9, 12, 12, 12, 9, 9, 9, 2, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 9, 9, 9, 9, 9, 9] 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, 54, 55, 56]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 3) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CO[C@@H]1[C@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C) `ZINC001435677501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435677501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001435677501 none CO[C@@H]1[C@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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.3', 'F', 'F', 'F', '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, 12, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 11, 11, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 11, 11, 11, 15, 15, 15, 11, 11, 11, 2, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 11, 11, 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, 51, 52, 53, 54, 55, 56]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435677501 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677501 Building ZINC001435677502 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435677502 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/4 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C) `ZINC001435677502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435677502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001435677502 none CO[C@@H]1[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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.3', 'F', 'F', 'F', '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, 12, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 14, 14, 3, 14, 14, 14, 14, 14, 14, 2, 2, 8, 8, 8, 18, 18, 18, 8, 8, 8, 2, 2, 2, 2, 14, 14, 4, 14, 2, 2, 2, 8, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 72 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/5 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C) `ZINC001435677502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435677502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001435677502 none CO[C@@H]1[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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.3', 'F', 'F', 'F', '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, 12, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 4, 18, 18, 18, 18, 18, 18, 4, 4, 6, 6, 6, 13, 13, 13, 6, 6, 6, 2, 4, 4, 4, 18, 18, 5, 18, 4, 4, 4, 6, 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, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435677502 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502 Building ZINC001435677502 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435677502 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 4) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C) `ZINC001435677502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435677502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001435677502 none CO[C@@H]1[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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.3', 'F', 'F', 'F', '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, 12, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 14, 14, 3, 14, 14, 14, 14, 14, 14, 2, 2, 8, 8, 8, 18, 18, 18, 8, 8, 8, 2, 2, 2, 2, 14, 14, 4, 14, 2, 2, 2, 8, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 72 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 5) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C) `ZINC001435677502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435677502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001435677502 none CO[C@@H]1[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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.3', 'F', 'F', 'F', '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, 12, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 4, 18, 18, 18, 18, 18, 18, 4, 4, 6, 6, 6, 13, 13, 13, 6, 6, 6, 2, 4, 4, 4, 18, 18, 5, 18, 4, 4, 4, 6, 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, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435677502 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677502 Building ZINC001435677503 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435677503 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/6 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1[C@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C) `ZINC001435677503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435677503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001435677503 none CO[C@@H]1[C@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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.3', 'F', 'F', 'F', '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, 12, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 9, 9, 9, 10, 10, 10, 9, 9, 9, 2, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 9, 9, 9, 9, 9, 9] 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, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/7 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1[C@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C) `ZINC001435677503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435677503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001435677503 none CO[C@@H]1[C@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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.3', 'F', 'F', 'F', '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, 12, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 9, 9, 9, 11, 11, 11, 9, 9, 9, 2, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 9, 9, 9, 9, 9, 9] 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, 54, 55, 56]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435677503 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503 Building ZINC001435677503 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435677503 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 6) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CO[C@@H]1[C@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C) `ZINC001435677503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435677503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001435677503 none CO[C@@H]1[C@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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.3', 'F', 'F', 'F', '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, 12, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 9, 9, 9, 10, 10, 10, 9, 9, 9, 2, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 9, 9, 9, 9, 9, 9] 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, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 7) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CO[C@@H]1[C@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C) `ZINC001435677503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435677503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001435677503 none CO[C@@H]1[C@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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.3', 'F', 'F', 'F', '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, 12, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 9, 9, 9, 11, 11, 11, 9, 9, 9, 2, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 9, 9, 9, 9, 9, 9] 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, 54, 55, 56]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435677503 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677503 Building ZINC001435677505 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435677505 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/8 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C) `ZINC001435677505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435677505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001435677505 none CO[C@@H]1[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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.3', 'F', 'F', 'F', '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, 12, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 8, 8, 8, 11, 11, 11, 8, 8, 8, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 8, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/9 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C) `ZINC001435677505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435677505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001435677505 none CO[C@@H]1[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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.3', 'F', 'F', 'F', '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, 12, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 9, 9, 9, 12, 12, 12, 9, 9, 9, 2, 2, 2, 2, 12, 12, 11, 12, 2, 2, 2, 9, 9, 9, 9, 9, 9] 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, 54, 55, 56]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435677505 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505 Building ZINC001435677505 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435677505 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 8) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CO[C@@H]1[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C) `ZINC001435677505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435677505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001435677505 none CO[C@@H]1[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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.3', 'F', 'F', 'F', '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, 12, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 8, 8, 8, 11, 11, 11, 8, 8, 8, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 8, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 9) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CO[C@@H]1[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C) `ZINC001435677505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435677505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001435677505 none CO[C@@H]1[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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.3', 'F', 'F', 'F', '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, 12, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 9, 9, 9, 12, 12, 12, 9, 9, 9, 2, 2, 2, 2, 12, 12, 11, 12, 2, 2, 2, 9, 9, 9, 9, 9, 9] 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, 54, 55, 56]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435677505 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435677505 Building ZINC001435694961 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435694961 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/10 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/10' -> `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](C(=O)OCc1ccccc1)C(C)(C)C) `ZINC001435694961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435694961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001435694961 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)OCc1ccccc1)C(C)(C)C 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.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 7, 7, 12, 34, 45, 45, 34, 45, 45, 6, 6, 6, 6, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 34, 34, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 6, 6, 6] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/11 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/11' -> `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](C(=O)OCc1ccccc1)C(C)(C)C) `ZINC001435694961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435694961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001435694961 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)OCc1ccccc1)C(C)(C)C 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.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 7, 7, 8, 26, 41, 41, 38, 41, 41, 5, 5, 5, 5, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 26, 26, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 5, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435694961 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961 Building ZINC001435694961 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435694961 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 10) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)OCc1ccccc1)C(C)(C)C) `ZINC001435694961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435694961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001435694961 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)OCc1ccccc1)C(C)(C)C 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.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 7, 7, 12, 34, 45, 45, 34, 45, 45, 6, 6, 6, 6, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 34, 34, 45, 45, 45, 45, 45, 6, 6, 6, 6, 6, 6, 6, 6, 6] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 11) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)OCc1ccccc1)C(C)(C)C) `ZINC001435694961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435694961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001435694961 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)OCc1ccccc1)C(C)(C)C 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.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 7, 7, 8, 26, 41, 41, 38, 41, 41, 5, 5, 5, 5, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 26, 26, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 5, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435694961 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435694961 Building ZINC001435700339 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435700339 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/12 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(Cl)c(Cl)c3)C2=O)cc1Cl) `ZINC001435700339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435700339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001435700339 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(Cl)c(Cl)c3)C2=O)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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 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: [11, 5, 2, 5, 5, 1, 1, 1, 1, 3, 3, 5, 9, 9, 9, 9, 9, 22, 22, 18, 22, 22, 22, 22, 9, 9, 5, 5, 5, 11, 11, 11, 5, 5, 3, 9, 9, 9, 9, 22, 22, 22, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/13 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(Cl)c(Cl)c3)C2=O)cc1Cl) `ZINC001435700339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435700339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001435700339 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(Cl)c(Cl)c3)C2=O)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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 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: [10, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 17, 17, 15, 17, 17, 17, 17, 8, 8, 6, 6, 6, 10, 10, 10, 6, 6, 2, 8, 8, 8, 8, 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, 41, 42]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435700339 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339 Building ZINC001435700339 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435700339 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 12) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)N[C@H]2CCN(c3ccc(Cl)c(Cl)c3)C2=O)cc1Cl) `ZINC001435700339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435700339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001435700339 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(Cl)c(Cl)c3)C2=O)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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 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: [11, 5, 2, 5, 5, 1, 1, 1, 1, 3, 3, 5, 9, 9, 9, 9, 9, 22, 22, 18, 22, 22, 22, 22, 9, 9, 5, 5, 5, 11, 11, 11, 5, 5, 3, 9, 9, 9, 9, 22, 22, 22, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 13) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)N[C@H]2CCN(c3ccc(Cl)c(Cl)c3)C2=O)cc1Cl) `ZINC001435700339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435700339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001435700339 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(c3ccc(Cl)c(Cl)c3)C2=O)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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 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: [10, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 17, 17, 15, 17, 17, 17, 17, 8, 8, 6, 6, 6, 10, 10, 10, 6, 6, 2, 8, 8, 8, 8, 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, 41, 42]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435700339 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700339 Building ZINC001435700340 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435700340 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/14 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(Cl)c(Cl)c3)C2=O)cc1Cl) `ZINC001435700340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435700340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001435700340 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(Cl)c(Cl)c3)C2=O)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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 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: [10, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 17, 17, 15, 17, 17, 17, 17, 8, 8, 6, 6, 6, 10, 10, 10, 6, 6, 2, 8, 8, 8, 8, 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, 41, 42]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/15 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(Cl)c(Cl)c3)C2=O)cc1Cl) `ZINC001435700340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435700340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001435700340 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(Cl)c(Cl)c3)C2=O)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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 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: [11, 5, 2, 5, 5, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 23, 23, 10, 10, 5, 5, 5, 11, 11, 11, 5, 5, 3, 10, 10, 10, 10, 23, 23, 23, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435700340 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340 Building ZINC001435700340 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435700340 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 14) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CCN(c3ccc(Cl)c(Cl)c3)C2=O)cc1Cl) `ZINC001435700340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435700340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001435700340 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(Cl)c(Cl)c3)C2=O)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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 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: [10, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 17, 17, 15, 17, 17, 17, 17, 8, 8, 6, 6, 6, 10, 10, 10, 6, 6, 2, 8, 8, 8, 8, 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, 41, 42]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 15) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CCN(c3ccc(Cl)c(Cl)c3)C2=O)cc1Cl) `ZINC001435700340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435700340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001435700340 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(c3ccc(Cl)c(Cl)c3)C2=O)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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 1, 1, 16, 7, 7, 7, 7, 7, 6, 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, 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: [11, 5, 2, 5, 5, 1, 1, 1, 1, 3, 3, 6, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 23, 23, 10, 10, 5, 5, 5, 11, 11, 11, 5, 5, 3, 10, 10, 10, 10, 23, 23, 23, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435700340 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435700340 Building ZINC001435703346 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435703346 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/16 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](C(N)=O)c1cccc(Br)c1) `ZINC001435703346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435703346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001435703346 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](C(N)=O)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 8, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 14, 14, 23, 23, 14, 46, 46, 32, 46, 46, 46, 6, 6, 6, 2, 1, 2, 23, 23, 46, 46, 46, 46] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/17 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](C(N)=O)c1cccc(Br)c1) `ZINC001435703346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435703346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001435703346 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](C(N)=O)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 8, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 16, 16, 19, 19, 16, 46, 46, 34, 46, 46, 46, 6, 6, 6, 3, 1, 3, 19, 19, 46, 46, 46, 46] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435703346 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346 Building ZINC001435703346 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435703346 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 16) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](C(N)=O)c1cccc(Br)c1) `ZINC001435703346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435703346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001435703346 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](C(N)=O)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 8, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 14, 14, 23, 23, 14, 46, 46, 32, 46, 46, 46, 6, 6, 6, 2, 1, 2, 23, 23, 46, 46, 46, 46] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 17) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](C(N)=O)c1cccc(Br)c1) `ZINC001435703346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435703346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001435703346 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@H](C(N)=O)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 8, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 16, 16, 19, 19, 16, 46, 46, 34, 46, 46, 46, 6, 6, 6, 3, 1, 3, 19, 19, 46, 46, 46, 46] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435703346 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703346 Building ZINC001435703350 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435703350 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/18 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](C(N)=O)c1cccc(Br)c1) `ZINC001435703350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435703350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001435703350 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](C(N)=O)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 8, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 16, 16, 19, 19, 16, 46, 46, 34, 46, 46, 46, 6, 6, 6, 3, 1, 3, 19, 19, 46, 46, 39, 46] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/19 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](C(N)=O)c1cccc(Br)c1) `ZINC001435703350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435703350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001435703350 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](C(N)=O)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 8, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 14, 14, 23, 23, 14, 46, 46, 32, 46, 46, 46, 6, 6, 6, 2, 1, 2, 23, 23, 46, 46, 32, 46] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435703350 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350 Building ZINC001435703350 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435703350 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 18) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](C(N)=O)c1cccc(Br)c1) `ZINC001435703350.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435703350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001435703350 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](C(N)=O)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 8, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens 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, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 16, 16, 19, 19, 16, 46, 46, 34, 46, 46, 46, 6, 6, 6, 3, 1, 3, 19, 19, 46, 46, 39, 46] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 19) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](C(N)=O)c1cccc(Br)c1) `ZINC001435703350.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435703350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001435703350 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)[C@@H](C(N)=O)c1cccc(Br)c1 NO_LONG_NAME dock atom types: ['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', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 8, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 1, 3, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 6, 14, 14, 23, 23, 14, 46, 46, 32, 46, 46, 46, 6, 6, 6, 2, 1, 2, 23, 23, 46, 46, 32, 46] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435703350 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435703350 Building ZINC001435709667 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001435709667 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/20 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC[C@H]1CC[N@](c2ccncc2)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435709667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435709667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435709667 none CN(CC[C@H]1CC[N@](c2ccncc2)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 8, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 14, 24, 24, 24, 24, 24, 34, 34, 24, 34, 34, 24, 24, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 24, 24, 24, 24, 34, 34, 34, 34, 24, 24, 24, 24, 3, 3] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/21 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC[C@H]1CC[N@@](c2ccncc2)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435709667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435709667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435709667 none CN(CC[C@H]1CC[N@@](c2ccncc2)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 8, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 14, 23, 23, 23, 23, 23, 34, 34, 23, 34, 34, 23, 23, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 23, 23, 23, 23, 34, 34, 34, 34, 23, 23, 23, 23, 3, 3] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/22 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/22' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC[C@H]1CC[N@](c2ccncc2)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435709667.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001435709667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435709667 none CN(CC[C@H]1CC[N@](c2ccncc2)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 8, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 14, 23, 23, 23, 23, 23, 33, 33, 33, 33, 33, 23, 23, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 23, 23, 23, 23, 33, 33, 33, 33, 23, 23, 23, 23, 3, 3] 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/23 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/23' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC[C@H]1CC[N@@](c2ccncc2)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435709667.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001435709667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435709667 none CN(CC[C@H]1CC[N@@](c2ccncc2)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 8, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 14, 23, 23, 23, 23, 23, 33, 33, 23, 33, 33, 23, 23, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 23, 23, 23, 23, 33, 33, 33, 33, 23, 23, 23, 23, 3, 3] 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435709667 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 Building ZINC001435709667 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001435709667 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 20) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(CC[C@H]1CC[N@](c2ccncc2)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435709667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435709667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435709667 none CN(CC[C@H]1CC[N@](c2ccncc2)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 8, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 14, 24, 24, 24, 24, 24, 34, 34, 24, 34, 34, 24, 24, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 24, 24, 24, 24, 34, 34, 34, 34, 24, 24, 24, 24, 3, 3] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 21) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(CC[C@H]1CC[N@@](c2ccncc2)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435709667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435709667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435709667 none CN(CC[C@H]1CC[N@@](c2ccncc2)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 8, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 14, 23, 23, 23, 23, 23, 34, 34, 23, 34, 34, 23, 23, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 23, 23, 23, 23, 34, 34, 34, 34, 23, 23, 23, 23, 3, 3] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 22) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC[C@H]1CC[N@](c2ccncc2)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435709667.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001435709667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435709667 none CN(CC[C@H]1CC[N@](c2ccncc2)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 8, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 14, 23, 23, 23, 23, 23, 33, 33, 33, 33, 33, 23, 23, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 23, 23, 23, 23, 33, 33, 33, 33, 23, 23, 23, 23, 3, 3] 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 23) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC[C@H]1CC[N@@](c2ccncc2)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435709667.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001435709667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435709667 none CN(CC[C@H]1CC[N@@](c2ccncc2)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 8, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 14, 23, 23, 23, 23, 23, 33, 33, 23, 33, 33, 23, 23, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 23, 23, 23, 23, 33, 33, 33, 33, 23, 23, 23, 23, 3, 3] 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435709667 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 Building ZINC001435709667 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001435709667 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 20) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(CC[C@H]1CC[N@](c2ccncc2)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435709667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435709667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435709667 none CN(CC[C@H]1CC[N@](c2ccncc2)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 8, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 14, 24, 24, 24, 24, 24, 34, 34, 24, 34, 34, 24, 24, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 24, 24, 24, 24, 34, 34, 34, 34, 24, 24, 24, 24, 3, 3] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 21) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(CC[C@H]1CC[N@@](c2ccncc2)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435709667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435709667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435709667 none CN(CC[C@H]1CC[N@@](c2ccncc2)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 8, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 14, 23, 23, 23, 23, 23, 34, 34, 23, 34, 34, 23, 23, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 23, 23, 23, 23, 34, 34, 34, 34, 23, 23, 23, 23, 3, 3] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 22) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC[C@H]1CC[N@](c2ccncc2)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435709667.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001435709667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435709667 none CN(CC[C@H]1CC[N@](c2ccncc2)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 8, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 14, 23, 23, 23, 23, 23, 33, 33, 33, 33, 33, 23, 23, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 23, 23, 23, 23, 33, 33, 33, 33, 23, 23, 23, 23, 3, 3] 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 23) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC[C@H]1CC[N@@](c2ccncc2)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435709667.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001435709667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435709667 none CN(CC[C@H]1CC[N@@](c2ccncc2)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 8, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 14, 23, 23, 23, 23, 23, 33, 33, 23, 33, 33, 23, 23, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 23, 23, 23, 23, 33, 33, 33, 33, 23, 23, 23, 23, 3, 3] 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435709667 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 Building ZINC001435709667 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001435709667 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 20) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(CC[C@H]1CC[N@](c2ccncc2)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435709667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435709667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435709667 none CN(CC[C@H]1CC[N@](c2ccncc2)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 8, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 14, 24, 24, 24, 24, 24, 34, 34, 24, 34, 34, 24, 24, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 24, 24, 24, 24, 34, 34, 34, 34, 24, 24, 24, 24, 3, 3] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 21) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(CC[C@H]1CC[N@@](c2ccncc2)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435709667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435709667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435709667 none CN(CC[C@H]1CC[N@@](c2ccncc2)CC1)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 8, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 14, 23, 23, 23, 23, 23, 34, 34, 23, 34, 34, 23, 23, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 23, 23, 23, 23, 34, 34, 34, 34, 23, 23, 23, 23, 3, 3] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 22) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC[C@H]1CC[N@](c2ccncc2)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435709667.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001435709667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435709667 none CN(CC[C@H]1CC[N@](c2ccncc2)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 8, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 14, 23, 23, 23, 23, 23, 33, 33, 33, 33, 33, 23, 23, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 23, 23, 23, 23, 33, 33, 33, 33, 23, 23, 23, 23, 3, 3] 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 23) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC[C@H]1CC[N@@](c2ccncc2)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435709667.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001435709667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435709667 none CN(CC[C@H]1CC[N@@](c2ccncc2)CC1)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 5, 8, 1, 1, 1, 8, 1, 1, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 14, 23, 23, 23, 23, 23, 33, 33, 23, 33, 33, 23, 23, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 10, 10, 10, 10, 23, 23, 23, 23, 33, 33, 33, 33, 23, 23, 23, 23, 3, 3] 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435709667 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435709667 Building ZINC001435757643 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435757643 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/24 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)[C@@H]1c1ccc(C(F)(F)F)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435757643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435757643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001435757643 none O=C(N1CCNC(=O)[C@@H]1c1ccc(C(F)(F)F)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 22, 22, 48, 48, 22, 22, 48, 48, 48, 48, 48, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 22, 22, 22, 22, 22, 48, 48, 48, 48, 6, 6, 6] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 283 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/25 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)[C@@H]1c1ccc(C(F)(F)F)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435757643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435757643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001435757643 none O=C(N1CCNC(=O)[C@@H]1c1ccc(C(F)(F)F)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 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] 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: [12, 3, 12, 20, 20, 20, 20, 20, 20, 20, 20, 41, 41, 25, 27, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 20, 20, 20, 20, 20, 41, 41, 41, 41, 6, 1, 6] 48 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435757643 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643 Building ZINC001435757643 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435757643 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 24) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCNC(=O)[C@@H]1c1ccc(C(F)(F)F)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435757643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435757643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001435757643 none O=C(N1CCNC(=O)[C@@H]1c1ccc(C(F)(F)F)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 22, 22, 22, 22, 22, 22, 22, 22, 48, 48, 22, 22, 48, 48, 48, 48, 48, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 22, 22, 22, 22, 22, 48, 48, 48, 48, 6, 6, 6] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 283 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 25) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCNC(=O)[C@@H]1c1ccc(C(F)(F)F)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435757643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435757643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001435757643 none O=C(N1CCNC(=O)[C@@H]1c1ccc(C(F)(F)F)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 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] 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: [12, 3, 12, 20, 20, 20, 20, 20, 20, 20, 20, 41, 41, 25, 27, 41, 41, 41, 41, 41, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 20, 20, 20, 20, 20, 41, 41, 41, 41, 6, 1, 6] 48 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435757643 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757643 Building ZINC001435757645 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435757645 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/26 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)[C@H]1c1ccc(C(F)(F)F)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435757645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435757645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001435757645 none O=C(N1CCNC(=O)[C@H]1c1ccc(C(F)(F)F)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 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] 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: [9, 2, 9, 14, 14, 14, 14, 14, 14, 14, 14, 26, 26, 22, 23, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 14, 14, 14, 14, 14, 26, 26, 26, 26, 6, 1, 6] 31 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/27 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)[C@H]1c1ccc(C(F)(F)F)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435757645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435757645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001435757645 none O=C(N1CCNC(=O)[C@H]1c1ccc(C(F)(F)F)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 33, 33, 23, 26, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 15, 15, 15, 15, 15, 33, 33, 33, 33, 6, 1, 6] 37 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435757645 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645 Building ZINC001435757645 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435757645 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 26) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)[C@H]1c1ccc(C(F)(F)F)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435757645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435757645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001435757645 none O=C(N1CCNC(=O)[C@H]1c1ccc(C(F)(F)F)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 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] 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: [9, 2, 9, 14, 14, 14, 14, 14, 14, 14, 14, 26, 26, 22, 23, 26, 26, 26, 26, 26, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 14, 14, 14, 14, 14, 26, 26, 26, 26, 6, 1, 6] 31 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 27) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)[C@H]1c1ccc(C(F)(F)F)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001435757645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435757645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001435757645 none O=C(N1CCNC(=O)[C@H]1c1ccc(C(F)(F)F)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 33, 33, 23, 26, 33, 33, 33, 33, 33, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 15, 15, 15, 15, 15, 33, 33, 33, 33, 6, 1, 6] 37 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435757645 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435757645 Building ZINC001435816001 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435816001 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/28 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2=O)ccc1Br) `ZINC001435816001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435816001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001435816001 none Cc1cc(N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2=O)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 24, 24, 24, 24, 24, 4, 24, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 3, 2, 2, 2, 2, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/29 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2=O)ccc1Br) `ZINC001435816001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435816001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001435816001 none Cc1cc(N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2=O)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 25, 25, 25, 25, 25, 4, 25, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 50, 50, 48, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 4, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435816001 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001 Building ZINC001435816001 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435816001 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 28) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cc(N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2=O)ccc1Br) `ZINC001435816001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435816001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001435816001 none Cc1cc(N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2=O)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 24, 24, 24, 24, 24, 4, 24, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 3, 2, 2, 2, 2, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 29) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cc(N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2=O)ccc1Br) `ZINC001435816001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435816001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001435816001 none Cc1cc(N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2=O)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 25, 25, 25, 25, 25, 4, 25, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 50, 50, 48, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 4, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435816001 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816001 Building ZINC001435816002 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435816002 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/30 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2=O)ccc1Br) `ZINC001435816002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435816002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001435816002 none Cc1cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2=O)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 26, 26, 26, 26, 26, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/31 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2=O)ccc1Br) `ZINC001435816002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435816002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001435816002 none Cc1cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2=O)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 24, 24, 24, 24, 24, 6, 24, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435816002 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002 Building ZINC001435816002 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435816002 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 30) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2=O)ccc1Br) `ZINC001435816002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435816002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001435816002 none Cc1cc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2=O)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 26, 26, 26, 26, 26, 7, 26, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 4, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 31) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2=O)ccc1Br) `ZINC001435816002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435816002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001435816002 none Cc1cc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2=O)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', '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, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 24, 24, 24, 24, 24, 6, 24, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435816002 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435816002 Building ZINC001435857338 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435857338 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/32 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CN2CCOCC2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435857338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435857338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435857338 none O=C(Nc1ccc(CN2CCOCC2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 12, 5, 5, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 11, 8, 11, 35, 35, 35, 35, 35, 35, 11, 11, 11, 1, 1, 1, 4, 4, 4, 4, 4, 2, 11, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 11, 4, 4] 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/33 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(CN2CCOCC2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435857338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435857338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435857338 none O=C(Nc1ccc(CN2CCOCC2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 12, 5, 5, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 10, 10, 10, 34, 35, 35, 35, 35, 35, 10, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 2, 10, 10, 34, 34, 35, 35, 35, 35, 35, 35, 35, 35, 10, 4, 4] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435857338 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338 Building ZINC001435857338 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435857338 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 32) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(CN2CCOCC2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435857338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435857338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435857338 none O=C(Nc1ccc(CN2CCOCC2)c(Cl)c1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 12, 5, 5, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 11, 11, 8, 11, 35, 35, 35, 35, 35, 35, 11, 11, 11, 1, 1, 1, 4, 4, 4, 4, 4, 2, 11, 11, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 11, 4, 4] 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 33) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(CN2CCOCC2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001435857338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435857338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001435857338 none O=C(Nc1ccc(CN2CCOCC2)c(Cl)c1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 10, 5, 5, 12, 5, 5, 1, 16, 1, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 10, 10, 10, 10, 34, 35, 35, 35, 35, 35, 10, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 2, 10, 10, 34, 34, 35, 35, 35, 35, 35, 35, 35, 35, 10, 4, 4] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435857338 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435857338 Building ZINC001435932040 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435932040 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/34 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(I)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001435932040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435932040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001435932040 none Cc1ccc(I)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 18, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 20, 20, 11, 20, 20, 11, 17, 17, 17, 17, 8, 17, 4, 11, 20, 20, 11, 20, 20, 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/35 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(I)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001435932040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435932040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001435932040 none Cc1ccc(I)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 18, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 20, 20, 11, 20, 20, 11, 17, 17, 17, 17, 14, 17, 4, 11, 20, 20, 20, 20, 20, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435932040 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040 Building ZINC001435932040 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435932040 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 34) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(I)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001435932040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435932040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001435932040 none Cc1ccc(I)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 18, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 20, 20, 11, 20, 20, 11, 17, 17, 17, 17, 8, 17, 4, 11, 20, 20, 11, 20, 20, 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 35) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(I)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001435932040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435932040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC001435932040 none Cc1ccc(I)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 18, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 17, 17, 17, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 20, 20, 11, 20, 20, 11, 17, 17, 17, 17, 14, 17, 4, 11, 20, 20, 20, 20, 20, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435932040 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435932040 Building ZINC001435974486 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435974486 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/36 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2o1) `ZINC001435974486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435974486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001435974486 none Cc1nc2cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 12, 12, 7, 12, 12, 7, 19, 19, 19, 19, 19, 19, 19, 4, 7, 12, 12, 7, 12, 12, 7] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/37 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2o1) `ZINC001435974486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435974486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001435974486 none Cc1nc2cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 12, 12, 7, 12, 12, 7, 19, 19, 19, 19, 19, 19, 19, 4, 7, 12, 12, 12, 12, 12, 7] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435974486 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486 Building ZINC001435974486 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435974486 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 36) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nc2cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2o1) `ZINC001435974486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435974486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001435974486 none Cc1nc2cc(Br)cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 12, 12, 7, 12, 12, 7, 19, 19, 19, 19, 19, 19, 19, 4, 7, 12, 12, 7, 12, 12, 7] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 37) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nc2cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2o1) `ZINC001435974486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435974486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001435974486 none Cc1nc2cc(Br)cc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 12, 12, 7, 12, 12, 7, 19, 19, 19, 19, 19, 19, 19, 4, 7, 12, 12, 12, 12, 12, 7] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435974486 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435974486 Building ZINC001435976519 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435976519 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/38 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)OC(C)C) `ZINC001435976519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435976519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001435976519 none COc1ccccc1[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 19, 26, 26, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 8, 19, 32, 35, 35, 28, 28, 28, 26, 26, 26, 26, 12, 12, 2, 8, 8, 35, 35, 35, 35, 35, 35, 35] 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: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/39 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)OC(C)C) `ZINC001435976519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435976519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001435976519 none COc1ccccc1[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 29, 29, 29, 18, 29, 29, 18, 12, 18, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 18, 31, 31, 31, 32, 32, 32, 29, 29, 29, 29, 12, 12, 3, 6, 6, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435976519 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519 Building ZINC001435976519 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435976519 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 38) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)OC(C)C) `ZINC001435976519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435976519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001435976519 none COc1ccccc1[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 19, 26, 26, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 8, 19, 32, 35, 35, 28, 28, 28, 26, 26, 26, 26, 12, 12, 2, 8, 8, 35, 35, 35, 35, 35, 35, 35] 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: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 39) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)OC(C)C) `ZINC001435976519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435976519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001435976519 none COc1ccccc1[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 29, 29, 29, 18, 29, 29, 18, 12, 18, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 18, 31, 31, 31, 32, 32, 32, 29, 29, 29, 29, 12, 12, 3, 6, 6, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435976519 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976519 Building ZINC001435976520 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435976520 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/40 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)OC(C)C) `ZINC001435976520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435976520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001435976520 none COc1ccccc1[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 18, 29, 29, 18, 12, 18, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 18, 31, 31, 31, 31, 31, 31, 29, 29, 29, 29, 12, 12, 3, 6, 6, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/41 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)OC(C)C) `ZINC001435976520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435976520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001435976520 none COc1ccccc1[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 19, 26, 26, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 8, 19, 32, 35, 35, 28, 28, 28, 26, 26, 26, 26, 12, 12, 2, 8, 8, 35, 35, 35, 35, 35, 35, 35] 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: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435976520 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520 Building ZINC001435976520 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435976520 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 40) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)OC(C)C) `ZINC001435976520.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435976520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001435976520 none COc1ccccc1[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 18, 29, 29, 18, 12, 18, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 18, 31, 31, 31, 31, 31, 31, 29, 29, 29, 29, 12, 12, 3, 6, 6, 31, 31, 31, 31, 31, 31, 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]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 41) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)OC(C)C) `ZINC001435976520.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435976520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001435976520 none COc1ccccc1[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)OC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 19, 26, 26, 19, 12, 19, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 8, 19, 32, 35, 35, 28, 28, 28, 26, 26, 26, 26, 12, 12, 2, 8, 8, 35, 35, 35, 35, 35, 35, 35] 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: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435976520 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435976520 Building ZINC001435981246 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435981246 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/42 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(C)(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001435981246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435981246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435981246 none CC(C)(C)OC(=O)N1CCC(C)(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 29, 18, 29, 18, 18, 18, 7, 17, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 18, 18, 37, 37, 37, 37, 37, 37, 37, 37, 37, 18, 18, 18, 18, 18, 18, 18, 4, 6, 6, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/43 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(C)(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001435981246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435981246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435981246 none CC(C)(C)OC(=O)N1CCC(C)(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 28, 19, 28, 19, 19, 19, 6, 17, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 19, 19, 19, 19, 19, 19, 19, 4, 7, 7, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435981246 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246 Building ZINC001435981246 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001435981246 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 42) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCC(C)(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001435981246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001435981246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435981246 none CC(C)(C)OC(=O)N1CCC(C)(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 29, 18, 29, 18, 18, 18, 7, 17, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 18, 18, 37, 37, 37, 37, 37, 37, 37, 37, 37, 18, 18, 18, 18, 18, 18, 18, 4, 6, 6, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 43) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCC(C)(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001435981246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001435981246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001435981246 none CC(C)(C)OC(=O)N1CCC(C)(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 28, 19, 28, 19, 19, 19, 6, 17, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 19, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 19, 19, 19, 19, 19, 19, 19, 4, 7, 7, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001435981246 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001435981246 Building ZINC001436017750 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436017750 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/44 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(CC(=O)N(C)C)cc1) `ZINC001436017750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436017750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436017750 none CC(C)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(CC(=O)N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 5, 1, 11, 8, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 6, 6, 5, 5, 21, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 6, 6, 21, 21, 33, 33, 33, 33, 33, 33, 6, 6] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 131 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/45 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(CC(=O)N(C)C)cc1) `ZINC001436017750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436017750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436017750 none CC(C)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(CC(=O)N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 5, 1, 11, 8, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 6, 6, 5, 6, 21, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 6, 6, 21, 21, 33, 33, 33, 33, 33, 33, 6, 6] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 133 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436017750 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750 Building ZINC001436017750 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436017750 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 44) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(CC(=O)N(C)C)cc1) `ZINC001436017750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436017750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436017750 none CC(C)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(CC(=O)N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 5, 1, 11, 8, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 6, 6, 5, 5, 21, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 6, 6, 21, 21, 33, 33, 33, 33, 33, 33, 6, 6] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 131 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 45) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(CC(=O)N(C)C)cc1) `ZINC001436017750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436017750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436017750 none CC(C)N(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccc(CC(=O)N(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 5, 1, 11, 8, 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, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 6, 6, 5, 6, 21, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 6, 6, 21, 21, 33, 33, 33, 33, 33, 33, 6, 6] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 133 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436017750 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436017750 Building ZINC001436045209 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436045209 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/46 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(I)c(Cl)c1) `ZINC001436045209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436045209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001436045209 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(I)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 1, 1, 18, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/47 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(I)c(Cl)c1) `ZINC001436045209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436045209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001436045209 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(I)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 1, 1, 18, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 20, 50, 50, 50, 50, 50, 50, 49, 2, 2, 2, 2, 2, 2, 3, 20, 20, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436045209 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209 Building ZINC001436045209 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436045209 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 46) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(I)c(Cl)c1) `ZINC001436045209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436045209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001436045209 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCc1ccc(I)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 1, 1, 18, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 19, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 19, 19, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 47) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(I)c(Cl)c1) `ZINC001436045209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436045209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001436045209 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCc1ccc(I)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 1, 1, 18, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 20, 50, 50, 50, 50, 50, 50, 49, 2, 2, 2, 2, 2, 2, 3, 20, 20, 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436045209 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436045209 Building ZINC001436121985 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436121985 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/48 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(OCc1ccccc1)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436121985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436121985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001436121985 none O=C(OCc1ccccc1)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 11, 28, 30, 30, 29, 30, 30, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 30, 30, 29, 30, 30, 4, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/49 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(OCc1ccccc1)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436121985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436121985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001436121985 none O=C(OCc1ccccc1)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 3, 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] 0 hydrogens 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, 13, 28, 33, 33, 28, 33, 33, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 28, 28, 33, 33, 28, 33, 33, 6, 6, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436121985 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985 Building ZINC001436121985 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436121985 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 48) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(OCc1ccccc1)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436121985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436121985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001436121985 none O=C(OCc1ccccc1)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 11, 28, 30, 30, 29, 30, 30, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 28, 28, 30, 30, 29, 30, 30, 4, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 49) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(OCc1ccccc1)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436121985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436121985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001436121985 none O=C(OCc1ccccc1)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 3, 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] 0 hydrogens 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, 13, 28, 33, 33, 28, 33, 33, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 28, 28, 33, 33, 28, 33, 33, 6, 6, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436121985 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121985 Building ZINC001436121986 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436121986 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/50 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(OCc1ccccc1)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436121986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436121986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001436121986 none O=C(OCc1ccccc1)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 3, 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] 0 hydrogens 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, 13, 28, 33, 33, 32, 33, 33, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 28, 28, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/51 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(OCc1ccccc1)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436121986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436121986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001436121986 none O=C(OCc1ccccc1)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 11, 29, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 29, 29, 30, 30, 30, 30, 30, 4, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436121986 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986 Building ZINC001436121986 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436121986 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 50) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(OCc1ccccc1)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436121986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436121986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001436121986 none O=C(OCc1ccccc1)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 3, 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] 0 hydrogens 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, 13, 28, 33, 33, 32, 33, 33, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 28, 28, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 51) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(OCc1ccccc1)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436121986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436121986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001436121986 none O=C(OCc1ccccc1)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [5, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 11, 29, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 29, 29, 30, 30, 30, 30, 30, 4, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436121986 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436121986 Building ZINC001436160032 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436160032 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/52 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)S(=O)(=O)c1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001436160032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436160032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001436160032 none CC(C)N(C)S(=O)(=O)c1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 20, 49, 3, 21, 20, 3, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 10, 10, 3, 3, 3, 3, 1, 3, 10, 10] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/53 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)S(=O)(=O)c1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001436160032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436160032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001436160032 none CC(C)N(C)S(=O)(=O)c1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 19, 49, 2, 19, 19, 2, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 10, 10, 2, 2, 2, 3, 1, 3, 10, 10] 50 rigid atoms, others: [12, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436160032 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032 Building ZINC001436160032 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436160032 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 52) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)N(C)S(=O)(=O)c1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001436160032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436160032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001436160032 none CC(C)N(C)S(=O)(=O)c1ccc(N(C)C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 20, 49, 3, 21, 20, 3, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 10, 10, 3, 3, 3, 3, 1, 3, 10, 10] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 53) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)N(C)S(=O)(=O)c1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001436160032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436160032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001436160032 none CC(C)N(C)S(=O)(=O)c1ccc(N(C)C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 8, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 19, 49, 2, 19, 19, 2, 10, 10, 2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 10, 10, 2, 2, 2, 3, 1, 3, 10, 10] 50 rigid atoms, others: [12, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436160032 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436160032 Building ZINC001436183570 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436183570 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/54 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436183570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436183570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001436183570 none CC(C)(C)OC(=O)NCC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 23, 32, 11, 7, 4, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 23, 11, 11, 7, 7, 4, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/55 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436183570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436183570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001436183570 none CC(C)(C)OC(=O)NCC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 33, 28, 33, 10, 8, 4, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 36, 36, 36, 36, 36, 36, 36, 36, 36, 28, 10, 10, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2] 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: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436183570 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570 Building ZINC001436183570 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436183570 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 54) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NCC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436183570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436183570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001436183570 none CC(C)(C)OC(=O)NCC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 23, 32, 11, 7, 4, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 23, 11, 11, 7, 7, 4, 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 55) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NCC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436183570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436183570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001436183570 none CC(C)(C)OC(=O)NCC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 33, 28, 33, 10, 8, 4, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 36, 36, 36, 36, 36, 36, 36, 36, 36, 28, 10, 10, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2] 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: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436183570 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183570 Building ZINC001436183571 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436183571 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/56 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436183571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436183571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001436183571 none CC(C)(C)OC(=O)NCC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 27, 33, 10, 8, 4, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 35, 27, 10, 10, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2] 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: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/57 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436183571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436183571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001436183571 none CC(C)(C)OC(=O)NCC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 22, 31, 10, 7, 4, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 22, 10, 10, 7, 7, 4, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436183571 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571 Building ZINC001436183571 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436183571 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 56) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NCC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436183571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436183571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001436183571 none CC(C)(C)OC(=O)NCC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 27, 33, 10, 8, 4, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 35, 35, 35, 27, 10, 10, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2] 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: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 57) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NCC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436183571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436183571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001436183571 none CC(C)(C)OC(=O)NCC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 22, 31, 10, 7, 4, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 22, 10, 10, 7, 7, 4, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436183571 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436183571 Building ZINC001436210932 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436210932 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/58 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436210932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210932 none O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 36, 39, 39, 39, 39, 39, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 36, 36, 39, 39, 39, 39, 39, 13, 13, 13, 13, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/59 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436210932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210932 none O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 36, 39, 39, 39, 39, 39, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 36, 36, 39, 39, 39, 39, 39, 13, 13, 13, 13, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/60 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/60' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210932.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436210932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210932 none O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 6, 15, 15, 15, 15, 15, 15, 15, 36, 39, 39, 36, 39, 39, 15, 15, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 36, 36, 39, 39, 37, 39, 39, 15, 15, 15, 15, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/61 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/61' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210932.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436210932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210932 none O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 6, 15, 15, 15, 15, 15, 15, 15, 36, 39, 39, 36, 39, 39, 15, 15, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 36, 36, 39, 39, 37, 39, 39, 15, 15, 15, 15, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436210932 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 Building ZINC001436210932 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436210932 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 58) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436210932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210932 none O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 36, 39, 39, 39, 39, 39, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 36, 36, 39, 39, 39, 39, 39, 13, 13, 13, 13, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 59) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436210932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210932 none O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 36, 39, 39, 39, 39, 39, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 36, 36, 39, 39, 39, 39, 39, 13, 13, 13, 13, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 60) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210932.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436210932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210932 none O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 6, 15, 15, 15, 15, 15, 15, 15, 36, 39, 39, 36, 39, 39, 15, 15, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 36, 36, 39, 39, 37, 39, 39, 15, 15, 15, 15, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 61) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/61: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210932.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436210932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210932 none O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 6, 15, 15, 15, 15, 15, 15, 15, 36, 39, 39, 36, 39, 39, 15, 15, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 36, 36, 39, 39, 37, 39, 39, 15, 15, 15, 15, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436210932 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 Building ZINC001436210932 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436210932 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 58) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436210932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210932 none O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 36, 39, 39, 39, 39, 39, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 36, 36, 39, 39, 39, 39, 39, 13, 13, 13, 13, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 59) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436210932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210932 none O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 36, 39, 39, 39, 39, 39, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 36, 36, 39, 39, 39, 39, 39, 13, 13, 13, 13, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 60) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210932.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436210932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210932 none O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 6, 15, 15, 15, 15, 15, 15, 15, 36, 39, 39, 36, 39, 39, 15, 15, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 36, 36, 39, 39, 37, 39, 39, 15, 15, 15, 15, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 61) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/61: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210932.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436210932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210932 none O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 6, 15, 15, 15, 15, 15, 15, 15, 36, 39, 39, 36, 39, 39, 15, 15, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 36, 36, 39, 39, 37, 39, 39, 15, 15, 15, 15, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436210932 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 Building ZINC001436210932 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436210932 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 58) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436210932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210932 none O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 36, 39, 39, 39, 39, 39, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 36, 36, 39, 39, 39, 39, 39, 13, 13, 13, 13, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 59) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436210932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210932 none O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 6, 13, 13, 13, 13, 13, 13, 13, 36, 39, 39, 39, 39, 39, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 36, 36, 39, 39, 39, 39, 39, 13, 13, 13, 13, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 60) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210932.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436210932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210932 none O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 6, 15, 15, 15, 15, 15, 15, 15, 36, 39, 39, 36, 39, 39, 15, 15, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 36, 36, 39, 39, 37, 39, 39, 15, 15, 15, 15, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 61) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/61: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210932.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436210932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210932 none O=C(N1CC[C@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 6, 15, 15, 15, 15, 15, 15, 15, 36, 39, 39, 36, 39, 39, 15, 15, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 36, 36, 39, 39, 37, 39, 39, 15, 15, 15, 15, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436210932 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210932 Building ZINC001436210935 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436210935 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/62 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436210935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210935 none O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 13, 13, 36, 39, 39, 39, 39, 39, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 36, 36, 39, 39, 39, 39, 39, 13, 13, 13, 13, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/63 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436210935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210935 none O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 13, 13, 36, 39, 39, 39, 39, 39, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 36, 36, 39, 39, 39, 39, 39, 13, 13, 13, 13, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/64 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/64' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210935.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436210935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210935 none O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 4, 12, 12, 12, 12, 12, 12, 12, 32, 36, 36, 36, 36, 36, 12, 12, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 32, 32, 36, 36, 36, 36, 36, 12, 12, 12, 12, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/65 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/65' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210935.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436210935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210935 none O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 4, 12, 12, 12, 12, 12, 12, 12, 32, 36, 36, 36, 36, 36, 12, 12, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 32, 32, 36, 36, 36, 36, 36, 12, 12, 12, 12, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436210935 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 Building ZINC001436210935 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436210935 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 62) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436210935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210935 none O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 13, 13, 36, 39, 39, 39, 39, 39, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 36, 36, 39, 39, 39, 39, 39, 13, 13, 13, 13, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 63) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436210935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210935 none O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 13, 13, 36, 39, 39, 39, 39, 39, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 36, 36, 39, 39, 39, 39, 39, 13, 13, 13, 13, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 64) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210935.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436210935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210935 none O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 4, 12, 12, 12, 12, 12, 12, 12, 32, 36, 36, 36, 36, 36, 12, 12, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 32, 32, 36, 36, 36, 36, 36, 12, 12, 12, 12, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 65) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210935.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436210935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210935 none O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 4, 12, 12, 12, 12, 12, 12, 12, 32, 36, 36, 36, 36, 36, 12, 12, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 32, 32, 36, 36, 36, 36, 36, 12, 12, 12, 12, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436210935 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 Building ZINC001436210935 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436210935 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 62) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436210935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210935 none O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 13, 13, 36, 39, 39, 39, 39, 39, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 36, 36, 39, 39, 39, 39, 39, 13, 13, 13, 13, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 63) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436210935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210935 none O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 13, 13, 36, 39, 39, 39, 39, 39, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 36, 36, 39, 39, 39, 39, 39, 13, 13, 13, 13, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 64) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210935.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436210935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210935 none O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 4, 12, 12, 12, 12, 12, 12, 12, 32, 36, 36, 36, 36, 36, 12, 12, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 32, 32, 36, 36, 36, 36, 36, 12, 12, 12, 12, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 65) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210935.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436210935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210935 none O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 4, 12, 12, 12, 12, 12, 12, 12, 32, 36, 36, 36, 36, 36, 12, 12, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 32, 32, 36, 36, 36, 36, 36, 12, 12, 12, 12, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436210935 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 Building ZINC001436210935 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001436210935 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 62) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436210935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210935 none O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 13, 13, 36, 39, 39, 39, 39, 39, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 36, 36, 39, 39, 39, 39, 39, 13, 13, 13, 13, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 63) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436210935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210935 none O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 13, 13, 36, 39, 39, 39, 39, 39, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 36, 36, 39, 39, 39, 39, 39, 13, 13, 13, 13, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 64) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210935.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001436210935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210935 none O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 4, 12, 12, 12, 12, 12, 12, 12, 32, 36, 36, 36, 36, 36, 12, 12, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 32, 32, 36, 36, 36, 36, 36, 12, 12, 12, 12, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 65) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436210935.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001436210935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436210935 none O=C(N1CC[C@@]2(CCN(Cc3ccccc3)C2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 4, 12, 12, 12, 12, 12, 12, 12, 32, 36, 36, 36, 36, 36, 12, 12, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 32, 32, 36, 36, 36, 36, 36, 12, 12, 12, 12, 3, 3] 50 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, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436210935 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436210935 Building ZINC001436222027 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436222027 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/66 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)c1c(Cl)cccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001436222027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436222027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436222027 none CC(C)S(=O)(=O)c1c(Cl)cccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', '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.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, 5, 5, 14, 11, 11, 1, 1, 16, 1, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 28, 10, 25, 25, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 9, 9, 7, 9, 9, 7, 28, 28, 28, 28, 28, 28, 28, 10, 10, 10, 4, 7, 9, 9, 7, 9, 9, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/67 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)c1c(Cl)cccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001436222027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436222027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436222027 none CC(C)S(=O)(=O)c1c(Cl)cccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', '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.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, 5, 5, 14, 11, 11, 1, 1, 16, 1, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens 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, 31, 10, 26, 26, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 9, 9, 7, 9, 9, 7, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 4, 7, 9, 9, 7, 9, 9, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436222027 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027 Building ZINC001436222027 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436222027 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 66) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)S(=O)(=O)c1c(Cl)cccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001436222027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436222027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436222027 none CC(C)S(=O)(=O)c1c(Cl)cccc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', '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.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, 5, 5, 14, 11, 11, 1, 1, 16, 1, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 28, 10, 25, 25, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 9, 9, 7, 9, 9, 7, 28, 28, 28, 28, 28, 28, 28, 10, 10, 10, 4, 7, 9, 9, 7, 9, 9, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 67) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)S(=O)(=O)c1c(Cl)cccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001436222027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436222027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436222027 none CC(C)S(=O)(=O)c1c(Cl)cccc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', '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.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, 5, 5, 14, 11, 11, 1, 1, 16, 1, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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] 0 hydrogens 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, 31, 10, 26, 26, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 9, 9, 7, 9, 9, 7, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 4, 7, 9, 9, 7, 9, 9, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436222027 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436222027 Building ZINC001436240854 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436240854 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/68 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)C(F)(F)F)cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001436240854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436240854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001436240854 none Cc1cc(CNC(=O)C(F)(F)F)cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', '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, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 2, 8, 8, 28, 48, 48, 48, 48, 48, 48, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 2, 28, 28, 48, 8, 2, 4, 4, 8] 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]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/69 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)C(F)(F)F)cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001436240854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436240854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001436240854 none Cc1cc(CNC(=O)C(F)(F)F)cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', '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, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 4, 8, 8, 27, 48, 48, 48, 48, 48, 48, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 27, 27, 48, 8, 2, 5, 5, 8] 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436240854 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854 Building ZINC001436240854 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436240854 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 68) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cc(CNC(=O)C(F)(F)F)cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001436240854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436240854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001436240854 none Cc1cc(CNC(=O)C(F)(F)F)cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', '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, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 2, 8, 8, 28, 48, 48, 48, 48, 48, 48, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 2, 28, 28, 48, 8, 2, 4, 4, 8] 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]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 69) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cc(CNC(=O)C(F)(F)F)cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001436240854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436240854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001436240854 none Cc1cc(CNC(=O)C(F)(F)F)cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', '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, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 4, 8, 8, 27, 48, 48, 48, 48, 48, 48, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 27, 27, 48, 8, 2, 5, 5, 8] 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]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436240854 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436240854 Building ZINC001436245457 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436245457 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/70 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1onc(c2ccccc2)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001436245457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436245457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001436245457 none CCOC(=O)c1onc(c2ccccc2)c1NC(=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', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 6, 13, 6, 6, 6, 6, 6, 18, 18, 6, 18, 18, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 22, 22, 22, 22, 22, 18, 18, 6, 18, 18, 4, 5, 5, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/71 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1onc(c2ccccc2)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001436245457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436245457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001436245457 none CCOC(=O)c1onc(c2ccccc2)c1NC(=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', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 6, 13, 6, 6, 6, 6, 6, 19, 19, 6, 19, 19, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 22, 22, 22, 22, 22, 19, 19, 7, 19, 19, 4, 5, 5, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436245457 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457 Building ZINC001436245457 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436245457 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 70) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1onc(c2ccccc2)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001436245457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436245457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001436245457 none CCOC(=O)c1onc(c2ccccc2)c1NC(=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', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 6, 13, 6, 6, 6, 6, 6, 18, 18, 6, 18, 18, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 22, 22, 22, 22, 22, 18, 18, 6, 18, 18, 4, 5, 5, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 71) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1onc(c2ccccc2)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001436245457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436245457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001436245457 none CCOC(=O)c1onc(c2ccccc2)c1NC(=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', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 6, 13, 6, 6, 6, 6, 6, 19, 19, 6, 19, 19, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 22, 22, 22, 22, 22, 19, 19, 7, 19, 19, 4, 5, 5, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436245457 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436245457 Building ZINC001436367406 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436367406 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/72 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436367406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436367406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001436367406 none COC(=O)c1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 12, 32, 12, 12, 7, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 32, 32, 32, 12, 12, 12, 4, 9, 9] 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/73 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436367406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436367406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001436367406 none COC(=O)c1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 12, 32, 12, 12, 8, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 32, 32, 32, 12, 12, 12, 4, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436367406 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406 Building ZINC001436367406 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436367406 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 72) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)c1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436367406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436367406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001436367406 none COC(=O)c1ccc(Br)cc1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 12, 32, 12, 12, 7, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 32, 32, 32, 12, 12, 12, 4, 9, 9] 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 73) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)c1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001436367406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436367406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001436367406 none COC(=O)c1ccc(Br)cc1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 12, 32, 12, 12, 8, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 32, 32, 32, 12, 12, 12, 4, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436367406 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436367406 Building ZINC001436382540 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436382540 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/74 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1c1nnc2nc(C)cc(C)n21) `ZINC001436382540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436382540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001436382540 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1c1nnc2nc(C)cc(C)n21 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', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 8, 1, 5, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 3, 5, 5, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 5, 5, 5, 5, 8, 21, 21, 21, 36, 36, 36, 36, 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/75 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1c1nnc2nc(C)cc(C)n21) `ZINC001436382540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436382540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001436382540 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1c1nnc2nc(C)cc(C)n21 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', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 8, 1, 5, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 3, 6, 6, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 7, 7, 6, 6, 6, 6, 7, 20, 20, 20, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436382540 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540 Building ZINC001436382540 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436382540 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 74) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1c1nnc2nc(C)cc(C)n21) `ZINC001436382540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436382540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001436382540 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1c1nnc2nc(C)cc(C)n21 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', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 8, 1, 5, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 3, 5, 5, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 5, 5, 5, 5, 8, 21, 21, 21, 36, 36, 36, 36, 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 75) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1c1nnc2nc(C)cc(C)n21) `ZINC001436382540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436382540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001436382540 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1c1nnc2nc(C)cc(C)n21 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', 'Cl', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 8, 1, 5, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 3, 6, 6, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 7, 7, 6, 6, 6, 6, 7, 20, 20, 20, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436382540 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436382540 Building ZINC001436384844 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436384844 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/76 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc1C(F)(F)F) `ZINC001436384844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436384844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001436384844 none CCOC(=O)c1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', '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', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 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, 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: [27, 16, 16, 4, 16, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 3, 4, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 2, 4, 4, 8, 8, 8, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/77 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc1C(F)(F)F) `ZINC001436384844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436384844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001436384844 none CCOC(=O)c1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', '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', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 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, 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: [26, 16, 16, 4, 16, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 2, 4, 4, 8, 8, 8, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436384844 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844 Building ZINC001436384844 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436384844 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 76) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc1C(F)(F)F) `ZINC001436384844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436384844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001436384844 none CCOC(=O)c1nc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', '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', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 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, 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: [27, 16, 16, 4, 16, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 3, 4, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 2, 4, 4, 8, 8, 8, 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 77) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc1C(F)(F)F) `ZINC001436384844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436384844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001436384844 none CCOC(=O)c1nc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)sc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', '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', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 14, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 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, 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: [26, 16, 16, 4, 16, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 2, 4, 4, 8, 8, 8, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436384844 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436384844 Building ZINC001436534732 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436534732 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/78 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c2nncn2ccc1C) `ZINC001436534732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436534732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001436534732 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c2nncn2ccc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 6, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 56 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/79 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c2nncn2ccc1C) `ZINC001436534732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436534732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001436534732 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c2nncn2ccc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 6, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 58 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436534732 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732 Building ZINC001436534732 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436534732 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 78) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c2nncn2ccc1C) `ZINC001436534732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436534732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001436534732 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c2nncn2ccc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 6, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 56 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 79) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c2nncn2ccc1C) `ZINC001436534732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436534732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001436534732 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c2nncn2ccc1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 6, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 58 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436534732 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436534732 Building ZINC001436571583 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436571583 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/80 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CC1CCOCC1)c1ccc(Br)cn1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436571583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436571583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001436571583 none O=C(N(CC1CCOCC1)c1ccc(Br)cn1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 17, 20, 20, 20, 20, 20, 5, 9, 9, 9, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 70 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/81 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CC1CCOCC1)c1ccc(Br)cn1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436571583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436571583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001436571583 none O=C(N(CC1CCOCC1)c1ccc(Br)cn1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 18, 19, 19, 19, 19, 19, 4, 9, 9, 9, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 67 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436571583 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583 Building ZINC001436571583 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436571583 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 80) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N(CC1CCOCC1)c1ccc(Br)cn1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436571583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436571583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001436571583 none O=C(N(CC1CCOCC1)c1ccc(Br)cn1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 17, 20, 20, 20, 20, 20, 5, 9, 9, 9, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 70 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 81) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N(CC1CCOCC1)c1ccc(Br)cn1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436571583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436571583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001436571583 none O=C(N(CC1CCOCC1)c1ccc(Br)cn1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 18, 19, 19, 19, 19, 19, 4, 9, 9, 9, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 67 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436571583 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436571583 Building ZINC001436612501 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436612501 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/82 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccc(C)cn1) `ZINC001436612501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436612501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001436612501 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccc(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/6899/xaj-8058088.10/working/building/ZINC001436612501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/83 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccc(C)cn1) `ZINC001436612501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436612501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001436612501 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccc(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/6899/xaj-8058088.10/working/building/ZINC001436612501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436612501 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501 Building ZINC001436612501 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436612501 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 82) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccc(C)cn1) `ZINC001436612501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436612501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001436612501 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1ccc(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/6899/xaj-8058088.10/working/building/ZINC001436612501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 83) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccc(C)cn1) `ZINC001436612501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436612501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001436612501 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1ccc(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/6899/xaj-8058088.10/working/building/ZINC001436612501 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436612501 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436612501 Building ZINC001436742201 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436742201 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/84 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(F)cc(I)cc1F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436742201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436742201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001436742201 none O=C(Nc1c(F)cc(I)cc1F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 15, 1, 1, 18, 1, 1, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 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, 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: [9, 1, 9, 9, 23, 23, 23, 16, 16, 23, 23, 23, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 9, 23, 23, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/85 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c(F)cc(I)cc1F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436742201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436742201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001436742201 none O=C(Nc1c(F)cc(I)cc1F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 15, 1, 1, 18, 1, 1, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 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, 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: [9, 1, 9, 9, 23, 23, 23, 9, 23, 23, 23, 23, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 9, 23, 23, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436742201 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201 Building ZINC001436742201 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436742201 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 84) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1c(F)cc(I)cc1F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436742201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436742201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001436742201 none O=C(Nc1c(F)cc(I)cc1F)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 15, 1, 1, 18, 1, 1, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 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, 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: [9, 1, 9, 9, 23, 23, 23, 16, 16, 23, 23, 23, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 9, 23, 23, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 85) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1c(F)cc(I)cc1F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001436742201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436742201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001436742201 none O=C(Nc1c(F)cc(I)cc1F)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 15, 1, 1, 18, 1, 1, 15, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 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, 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: [9, 1, 9, 9, 23, 23, 23, 9, 23, 23, 23, 23, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 9, 23, 23, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436742201 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436742201 Building ZINC001436865129 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436865129 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/86 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nn(CC(F)(F)F)cc2Br)cc1Cl) `ZINC001436865129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436865129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001436865129 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nn(CC(F)(F)F)cc2Br)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.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 5, 5, 15, 15, 15, 1, 1, 17, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 18, 18, 18, 18, 5, 5, 5, 6, 6, 6, 13, 13, 13, 6, 6, 2, 18, 18, 5, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/87 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nn(CC(F)(F)F)cc2Br)cc1Cl) `ZINC001436865129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436865129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001436865129 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nn(CC(F)(F)F)cc2Br)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.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 5, 5, 15, 15, 15, 1, 1, 17, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 18, 18, 18, 18, 5, 5, 5, 6, 6, 6, 13, 13, 13, 6, 6, 2, 18, 18, 5, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436865129 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129 Building ZINC001436865129 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436865129 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 86) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)Nc2nn(CC(F)(F)F)cc2Br)cc1Cl) `ZINC001436865129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436865129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001436865129 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2nn(CC(F)(F)F)cc2Br)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.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 5, 5, 15, 15, 15, 1, 1, 17, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 18, 18, 18, 18, 5, 5, 5, 6, 6, 6, 13, 13, 13, 6, 6, 2, 18, 18, 5, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 87) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)Nc2nn(CC(F)(F)F)cc2Br)cc1Cl) `ZINC001436865129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436865129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001436865129 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2nn(CC(F)(F)F)cc2Br)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.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'Br', 'C.ar', 'C.ar', 'Cl', '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, 8, 8, 5, 5, 15, 15, 15, 1, 1, 17, 1, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 18, 18, 18, 18, 5, 5, 5, 6, 6, 6, 13, 13, 13, 6, 6, 2, 18, 18, 5, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436865129 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436865129 Building ZINC001436957375 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436957375 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/88 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/88' -> `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](CC(C)C)C(=O)OC(C)(C)C) `ZINC001436957375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436957375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001436957375 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](CC(C)C)C(=O)OC(C)(C)C 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', 'C.3', 'C.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', '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, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 5, 5, 5, 10, 13, 13, 18, 18, 18, 13, 37, 37, 38, 38, 38, 38, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 5, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 38, 38, 38, 38, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 148 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/89 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/89' -> `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](CC(C)C)C(=O)OC(C)(C)C) `ZINC001436957375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436957375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001436957375 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](CC(C)C)C(=O)OC(C)(C)C 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', 'C.3', 'C.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', '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, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 9, 9, 9, 6, 25, 25, 25, 25, 25, 25, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 115 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436957375 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375 Building ZINC001436957375 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436957375 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 88) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](CC(C)C)C(=O)OC(C)(C)C) `ZINC001436957375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436957375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001436957375 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](CC(C)C)C(=O)OC(C)(C)C 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', 'C.3', 'C.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', '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, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 5, 5, 5, 10, 13, 13, 18, 18, 18, 13, 37, 37, 38, 38, 38, 38, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 5, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 18, 38, 38, 38, 38, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 148 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 89) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](CC(C)C)C(=O)OC(C)(C)C) `ZINC001436957375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436957375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001436957375 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](CC(C)C)C(=O)OC(C)(C)C 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', 'C.3', 'C.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', '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, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 6, 6, 9, 9, 9, 6, 25, 25, 25, 25, 25, 25, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 115 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436957375 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957375 Building ZINC001436957376 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436957376 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/90 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/90' -> `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](CC(C)C)C(=O)OC(C)(C)C) `ZINC001436957376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436957376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001436957376 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](CC(C)C)C(=O)OC(C)(C)C 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', 'C.3', 'C.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', '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, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 9, 9, 11, 11, 11, 9, 30, 30, 30, 30, 30, 30, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 128 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/91 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/91' -> `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](CC(C)C)C(=O)OC(C)(C)C) `ZINC001436957376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436957376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001436957376 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](CC(C)C)C(=O)OC(C)(C)C 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', 'C.3', 'C.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', '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, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 9, 9, 13, 13, 13, 9, 35, 35, 40, 41, 41, 41, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 41, 41, 41, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436957376 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376 Building ZINC001436957376 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436957376 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 90) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](CC(C)C)C(=O)OC(C)(C)C) `ZINC001436957376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436957376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001436957376 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](CC(C)C)C(=O)OC(C)(C)C 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', 'C.3', 'C.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', '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, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 9, 9, 11, 11, 11, 9, 30, 30, 30, 30, 30, 30, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 128 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 91) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](CC(C)C)C(=O)OC(C)(C)C) `ZINC001436957376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436957376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001436957376 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](CC(C)C)C(=O)OC(C)(C)C 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', 'C.3', 'C.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', '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, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 9, 9, 13, 13, 13, 9, 35, 35, 40, 41, 41, 41, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 41, 41, 41, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436957376 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436957376 Building ZINC001436994121 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436994121 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/92 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc(C(F)(F)F)c2)n[nH]1) `ZINC001436994121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436994121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436994121 none Cc1nc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc(C(F)(F)F)c2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 2, 6, 6, 6, 6, 6, 6, 6, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/93 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc(C(F)(F)F)c2)n[nH]1) `ZINC001436994121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436994121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436994121 none Cc1nc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc(C(F)(F)F)c2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 2, 6, 6, 6, 6, 6, 6, 6, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436994121 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121 Building ZINC001436994121 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001436994121 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 92) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc(C(F)(F)F)c2)n[nH]1) `ZINC001436994121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001436994121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436994121 none Cc1nc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc(C(F)(F)F)c2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 2, 6, 6, 6, 6, 6, 6, 6, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 93) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc(C(F)(F)F)c2)n[nH]1) `ZINC001436994121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001436994121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001436994121 none Cc1nc(c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)cc(C(F)(F)F)c2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 11, 2, 6, 6, 6, 6, 6, 6, 6, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001436994121 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001436994121 Building ZINC001437111806 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437111806 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/94 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(N(Cc2ccccn2)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC1) `ZINC001437111806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437111806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001437111806 none CC(C)(C)OC(=O)N1CCC(N(Cc2ccccn2)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 16, 6, 6, 6, 5, 2, 5, 12, 14, 14, 14, 14, 14, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 12, 12, 14, 14, 14, 14, 2, 2, 2, 2, 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/95 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(N(Cc2ccccn2)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC1) `ZINC001437111806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437111806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001437111806 none CC(C)(C)OC(=O)N1CCC(N(Cc2ccccn2)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 17, 8, 17, 8, 8, 8, 5, 2, 6, 12, 14, 14, 14, 14, 14, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 8, 8, 12, 12, 14, 14, 14, 14, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [54, 55, 19, 52, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 56, 57, 58, 59]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437111806 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806 Building ZINC001437111806 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437111806 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 94) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)(C)OC(=O)N1CCC(N(Cc2ccccn2)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC1) `ZINC001437111806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437111806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001437111806 none CC(C)(C)OC(=O)N1CCC(N(Cc2ccccn2)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 16, 6, 6, 6, 5, 2, 5, 12, 14, 14, 14, 14, 14, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 12, 12, 14, 14, 14, 14, 2, 2, 2, 2, 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 95) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)(C)OC(=O)N1CCC(N(Cc2ccccn2)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC1) `ZINC001437111806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437111806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001437111806 none CC(C)(C)OC(=O)N1CCC(N(Cc2ccccn2)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 17, 8, 17, 8, 8, 8, 5, 2, 6, 12, 14, 14, 14, 14, 14, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 8, 8, 8, 12, 12, 14, 14, 14, 14, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [54, 55, 19, 52, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 56, 57, 58, 59]) total number of confs: 120 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437111806 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437111806 Building ZINC001437249779 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437249779 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/96 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/96' -> `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)Nc1ncc2[nH]ccc2c1Br) `ZINC001437249779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437249779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001437249779 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncc2[nH]ccc2c1Br 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.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', '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, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 17, 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, 4, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 14, 14, 7, 14, 14, 5, 5, 1, 1, 1, 1, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 14, 14, 5, 14, 14, 5, 5, 5, 9, 30, 30, 30] 48 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]) total number of confs: 78 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/97 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/97' -> `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)Nc1ncc2[nH]ccc2c1Br) `ZINC001437249779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437249779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001437249779 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncc2[nH]ccc2c1Br 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.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', '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, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 17, 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, 4, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 5, 5, 1, 1, 1, 1, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 15, 15, 8, 15, 15, 5, 5, 5, 9, 29, 29, 29] 48 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]) total number of confs: 92 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437249779 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779 Building ZINC001437249779 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437249779 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 96) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncc2[nH]ccc2c1Br) `ZINC001437249779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437249779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001437249779 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncc2[nH]ccc2c1Br 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.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', '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, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 17, 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, 4, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 14, 14, 7, 14, 14, 5, 5, 1, 1, 1, 1, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 14, 14, 5, 14, 14, 5, 5, 5, 9, 30, 30, 30] 48 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]) total number of confs: 78 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 97) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncc2[nH]ccc2c1Br) `ZINC001437249779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437249779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001437249779 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncc2[nH]ccc2c1Br 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.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', '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, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 17, 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, 4, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 15, 15, 5, 15, 15, 5, 5, 1, 1, 1, 1, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 15, 15, 8, 15, 15, 5, 5, 5, 9, 29, 29, 29] 48 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]) total number of confs: 92 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437249779 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437249779 Building ZINC001437307205 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437307205 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/98 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1nccc(c2sccc2Br)n1) `ZINC001437307205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437307205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001437307205 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1nccc(c2sccc2Br)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'Br', 'N.ar', 'H', '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, 1, 1, 1, 1, 14, 1, 1, 1, 17, 8, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 50, 50] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/99 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1nccc(c2sccc2Br)n1) `ZINC001437307205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437307205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001437307205 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1nccc(c2sccc2Br)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'Br', 'N.ar', 'H', '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, 1, 1, 1, 1, 14, 1, 1, 1, 17, 8, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 50, 50] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437307205 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205 Building ZINC001437307205 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437307205 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 98) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1nccc(c2sccc2Br)n1) `ZINC001437307205.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437307205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001437307205 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)c1nccc(c2sccc2Br)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'Br', 'N.ar', 'H', '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, 1, 1, 1, 1, 14, 1, 1, 1, 17, 8, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 50, 50] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 99) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1nccc(c2sccc2Br)n1) `ZINC001437307205.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437307205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001437307205 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)c1nccc(c2sccc2Br)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', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'Br', 'N.ar', 'H', '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, 1, 1, 1, 1, 14, 1, 1, 1, 17, 8, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 50, 50] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437307205 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437307205 Building ZINC001437510322 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437510322 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/100 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc2c(c1)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)CCC2) `ZINC001437510322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437510322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001437510322 none COC(=O)c1ccc2c(c1)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)CCC2 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 11, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 44, 37, 37, 37, 37, 37, 37, 14, 37, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 37, 37, 37, 44, 44, 44, 37, 37, 37, 14, 14, 2, 6, 6, 37, 37, 37, 37, 37, 37] 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]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/101 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc2c(c1)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)CCC2) `ZINC001437510322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437510322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001437510322 none COC(=O)c1ccc2c(c1)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)CCC2 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 11, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 43, 33, 33, 33, 33, 33, 33, 14, 33, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 33, 33, 33, 43, 43, 43, 33, 33, 33, 14, 14, 3, 6, 6, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437510322 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322 Building ZINC001437510322 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437510322 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 100) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)c1ccc2c(c1)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)CCC2) `ZINC001437510322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437510322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001437510322 none COC(=O)c1ccc2c(c1)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)CCC2 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 11, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 44, 37, 37, 37, 37, 37, 37, 14, 37, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 37, 37, 37, 44, 44, 44, 37, 37, 37, 14, 14, 2, 6, 6, 37, 37, 37, 37, 37, 37] 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]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 101) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)c1ccc2c(c1)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)CCC2) `ZINC001437510322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437510322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001437510322 none COC(=O)c1ccc2c(c1)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)CCC2 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 11, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 43, 33, 33, 33, 33, 33, 33, 14, 33, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 33, 33, 33, 43, 43, 43, 33, 33, 33, 14, 14, 3, 6, 6, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437510322 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510322 Building ZINC001437510326 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437510326 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/102 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc2c(c1)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)CCC2) `ZINC001437510326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437510326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001437510326 none COC(=O)c1ccc2c(c1)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)CCC2 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 11, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 43, 31, 31, 31, 31, 31, 31, 13, 31, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 31, 43, 43, 43, 31, 31, 31, 13, 13, 2, 6, 6, 31, 31, 31, 31, 31, 31] 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]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/103 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccc2c(c1)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)CCC2) `ZINC001437510326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437510326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001437510326 none COC(=O)c1ccc2c(c1)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)CCC2 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 11, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 44, 37, 37, 37, 37, 37, 37, 13, 37, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 37, 37, 37, 44, 44, 44, 37, 37, 37, 13, 13, 2, 6, 6, 37, 37, 37, 37, 37, 37] 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]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437510326 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326 Building ZINC001437510326 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437510326 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 102) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)c1ccc2c(c1)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)CCC2) `ZINC001437510326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437510326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001437510326 none COC(=O)c1ccc2c(c1)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)CCC2 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 11, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 43, 31, 31, 31, 31, 31, 31, 13, 31, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 31, 43, 43, 43, 31, 31, 31, 13, 13, 2, 6, 6, 31, 31, 31, 31, 31, 31] 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]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 103) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)c1ccc2c(c1)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)CCC2) `ZINC001437510326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437510326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001437510326 none COC(=O)c1ccc2c(c1)[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)CCC2 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 11, 1, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 44, 37, 37, 37, 37, 37, 37, 13, 37, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 37, 37, 37, 44, 44, 44, 37, 37, 37, 13, 13, 2, 6, 6, 37, 37, 37, 37, 37, 37] 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]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437510326 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437510326 Building ZINC001437520308 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437520308 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/104 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F) `ZINC001437520308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437520308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001437520308 none O=C(N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 15, 15, 15, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 11, 20, 11, 12, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 5, 5, 5, 5, 5, 20, 28, 28, 28, 28, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 20, 20] 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]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/105 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F) `ZINC001437520308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437520308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001437520308 none O=C(N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 15, 15, 15, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 7, 21, 7, 8, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 21, 31, 31, 31, 31, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 21, 21] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437520308 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308 Building ZINC001437520308 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437520308 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 104) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F) `ZINC001437520308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437520308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001437520308 none O=C(N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 15, 15, 15, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 20, 11, 20, 11, 12, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 5, 5, 5, 5, 5, 20, 28, 28, 28, 28, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 20, 20] 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]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 105) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F) `ZINC001437520308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437520308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001437520308 none O=C(N1CCC[C@@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 15, 15, 15, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 7, 21, 7, 8, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 21, 31, 31, 31, 31, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 21, 21] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437520308 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520308 Building ZINC001437520310 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437520310 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/106 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F) `ZINC001437520310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437520310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001437520310 none O=C(N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 15, 15, 15, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 11, 22, 11, 13, 11, 11, 11, 11, 11, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 22, 32, 32, 32, 32, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 22, 22] 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]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/107 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F) `ZINC001437520310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437520310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001437520310 none O=C(N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 15, 15, 15, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 19, 19, 19, 19, 10, 19, 10, 11, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 5, 5, 5, 5, 5, 19, 27, 27, 27, 27, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 19, 19] 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]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437520310 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310 Building ZINC001437520310 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437520310 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 106) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F) `ZINC001437520310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437520310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001437520310 none O=C(N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 15, 15, 15, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 11, 22, 11, 13, 11, 11, 11, 11, 11, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 22, 32, 32, 32, 32, 22, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 22, 22] 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]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 107) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F) `ZINC001437520310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437520310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001437520310 none O=C(N1CCC[C@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 15, 15, 15, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 19, 19, 19, 19, 10, 19, 10, 11, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 5, 5, 5, 5, 5, 19, 27, 27, 27, 27, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 19, 19] 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]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437520310 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520310 Building ZINC001437520312 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437520312 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/108 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F) `ZINC001437520312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437520312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001437520312 none O=C(N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 15, 15, 15, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 17, 17, 17, 17, 6, 17, 6, 8, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 17, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 17, 17] 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]) total number of confs: 105 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/109 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F) `ZINC001437520312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437520312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001437520312 none O=C(N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 15, 15, 15, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 6, 16, 6, 8, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 16, 29, 29, 29, 29, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 16, 16] 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]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437520312 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312 Building ZINC001437520312 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437520312 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 108) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F) `ZINC001437520312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437520312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001437520312 none O=C(N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 15, 15, 15, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 17, 17, 17, 17, 6, 17, 6, 8, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 17, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 17, 17] 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]) total number of confs: 105 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 109) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F) `ZINC001437520312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437520312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001437520312 none O=C(N1CCC[C@H]([C@@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 15, 15, 15, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 16, 16, 16, 16, 6, 16, 6, 8, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 16, 29, 29, 29, 29, 16, 16, 16, 16, 16, 16, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 16, 16] 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]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437520312 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520312 Building ZINC001437520313 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437520313 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/110 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F) `ZINC001437520313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437520313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001437520313 none O=C(N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 15, 15, 15, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 5, 21, 5, 7, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 21, 29, 29, 29, 29, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 21, 21] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 88 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/111 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F) `ZINC001437520313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437520313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001437520313 none O=C(N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 15, 15, 15, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 7, 21, 7, 8, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 21, 29, 29, 29, 29, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 21, 21] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 89 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437520313 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313 Building ZINC001437520313 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437520313 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 110) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/110: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F) `ZINC001437520313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437520313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001437520313 none O=C(N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 15, 15, 15, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 5, 21, 5, 7, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 21, 29, 29, 29, 29, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 21, 21] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 88 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 111) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/111: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F) `ZINC001437520313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437520313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001437520313 none O=C(N1CCC[C@@H]([C@H]2CCCCN2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', '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', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 15, 15, 15, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 7, 21, 7, 8, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 21, 29, 29, 29, 29, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 21, 21] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 89 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437520313 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437520313 Building ZINC001437543966 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437543966 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/112 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)(C1CCC1)C(F)(F)F) `ZINC001437543966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437543966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001437543966 none CCOC(=O)[C@@](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)(C1CCC1)C(F)(F)F 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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 25, 10, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 18, 18, 18, 10, 10, 10, 10, 41, 41, 41, 41, 41, 4, 3, 1, 3, 18, 18, 18, 18, 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, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/113 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)(C1CCC1)C(F)(F)F) `ZINC001437543966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437543966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001437543966 none CCOC(=O)[C@@](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)(C1CCC1)C(F)(F)F 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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 25, 10, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 17, 17, 17, 10, 10, 10, 10, 39, 39, 39, 39, 39, 4, 3, 1, 3, 17, 17, 17, 17, 17, 17, 17] 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: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437543966 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966 Building ZINC001437543966 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437543966 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 112) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)[C@@](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)(C1CCC1)C(F)(F)F) `ZINC001437543966.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437543966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001437543966 none CCOC(=O)[C@@](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)(C1CCC1)C(F)(F)F 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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 25, 10, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 18, 18, 18, 10, 10, 10, 10, 41, 41, 41, 41, 41, 4, 3, 1, 3, 18, 18, 18, 18, 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, 37, 38, 39, 40, 41, 42]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 113) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)[C@@](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)(C1CCC1)C(F)(F)F) `ZINC001437543966.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437543966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001437543966 none CCOC(=O)[C@@](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)(C1CCC1)C(F)(F)F 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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 25, 10, 25, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 17, 17, 17, 10, 10, 10, 10, 39, 39, 39, 39, 39, 4, 3, 1, 3, 17, 17, 17, 17, 17, 17, 17] 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: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437543966 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543966 Building ZINC001437543972 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437543972 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/114 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)(C1CCC1)C(F)(F)F) `ZINC001437543972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437543972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001437543972 none CCOC(=O)[C@](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)(C1CCC1)C(F)(F)F 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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 23, 23, 9, 23, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 16, 16, 16, 9, 9, 9, 9, 38, 38, 38, 38, 38, 4, 3, 1, 3, 16, 16, 16, 16, 16, 16, 16] 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: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/115 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)(C1CCC1)C(F)(F)F) `ZINC001437543972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437543972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001437543972 none CCOC(=O)[C@](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)(C1CCC1)C(F)(F)F 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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 23, 23, 11, 23, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 18, 18, 18, 11, 11, 11, 11, 37, 37, 37, 37, 37, 4, 3, 1, 3, 18, 18, 18, 18, 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, 37, 38, 39, 40, 41, 42]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437543972 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972 Building ZINC001437543972 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437543972 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 114) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)[C@](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)(C1CCC1)C(F)(F)F) `ZINC001437543972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437543972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001437543972 none CCOC(=O)[C@](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)(C1CCC1)C(F)(F)F 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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 23, 23, 9, 23, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 16, 16, 16, 9, 9, 9, 9, 38, 38, 38, 38, 38, 4, 3, 1, 3, 16, 16, 16, 16, 16, 16, 16] 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: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 115) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)[C@](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)(C1CCC1)C(F)(F)F) `ZINC001437543972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437543972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001437543972 none CCOC(=O)[C@](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)(C1CCC1)C(F)(F)F 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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', '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, 1, 16, 1, 1, 16, 1, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 23, 23, 11, 23, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 18, 18, 18, 11, 11, 11, 11, 37, 37, 37, 37, 37, 4, 3, 1, 3, 18, 18, 18, 18, 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, 37, 38, 39, 40, 41, 42]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437543972 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437543972 Building ZINC001437549684 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437549684 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/116 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](c2ccccc2)[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC001437549684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437549684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001437549684 none CC(C)(C)OC(=O)N1CC[C@H](c2ccccc2)[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 24, 41, 24, 24, 24, 24, 24, 24, 26, 26, 24, 26, 26, 9, 24, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 26, 26, 24, 26, 26, 3, 3, 3, 3, 3, 24, 24] 50 rigid atoms, others: [21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 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: 150 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/117 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](c2ccccc2)[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC001437549684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437549684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001437549684 none CC(C)(C)OC(=O)N1CC[C@H](c2ccccc2)[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 41, 24, 41, 24, 24, 24, 24, 24, 24, 26, 26, 24, 26, 26, 10, 24, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 24, 49, 49, 49, 49, 49, 49, 49, 49, 49, 24, 24, 24, 24, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 24, 24] 50 rigid atoms, others: [21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 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: 152 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437549684 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684 Building ZINC001437549684 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437549684 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 116) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@H](c2ccccc2)[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC001437549684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437549684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001437549684 none CC(C)(C)OC(=O)N1CC[C@H](c2ccccc2)[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 24, 41, 24, 24, 24, 24, 24, 24, 26, 26, 24, 26, 26, 9, 24, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 26, 26, 24, 26, 26, 3, 3, 3, 3, 3, 24, 24] 50 rigid atoms, others: [21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 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: 150 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 117) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@H](c2ccccc2)[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC001437549684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437549684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001437549684 none CC(C)(C)OC(=O)N1CC[C@H](c2ccccc2)[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 41, 24, 41, 24, 24, 24, 24, 24, 24, 26, 26, 24, 26, 26, 10, 24, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 24, 49, 49, 49, 49, 49, 49, 49, 49, 49, 24, 24, 24, 24, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 24, 24] 50 rigid atoms, others: [21, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 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: 152 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437549684 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437549684 Building ZINC001437553943 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437553943 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/118 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1c1ccccc1) `ZINC001437553943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437553943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001437553943 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1c1ccccc1 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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 12, 25, 25, 25, 25, 39, 39, 47, 47, 47, 47, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 6, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 25, 25, 25, 25, 25, 25, 25, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/119 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1c1ccccc1) `ZINC001437553943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437553943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001437553943 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1c1ccccc1 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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 11, 25, 25, 25, 25, 40, 40, 47, 47, 47, 47, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 3, 3, 3, 3, 3, 3, 3, 5, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 25, 25, 25, 25, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437553943 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943 Building ZINC001437553943 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437553943 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 118) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1c1ccccc1) `ZINC001437553943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437553943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001437553943 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1c1ccccc1 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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 12, 25, 25, 25, 25, 39, 39, 47, 47, 47, 47, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 4, 4, 4, 6, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 25, 25, 25, 25, 25, 25, 25, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 119) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/119: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1c1ccccc1) `ZINC001437553943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437553943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001437553943 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1c1ccccc1 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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 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, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 11, 25, 25, 25, 25, 40, 40, 47, 47, 47, 47, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 3, 3, 3, 3, 3, 3, 3, 5, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 25, 25, 25, 25, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437553943 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437553943 Building ZINC001437627770 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437627770 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/120 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(Cl)ccc1I)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001437627770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437627770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001437627770 none O=C(NCc1cc(Cl)ccc1I)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 16, 1, 1, 1, 18, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 11, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/121 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc(Cl)ccc1I)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001437627770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437627770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001437627770 none O=C(NCc1cc(Cl)ccc1I)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 16, 1, 1, 1, 18, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 11, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437627770 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770 Building ZINC001437627770 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437627770 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 120) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(NCc1cc(Cl)ccc1I)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001437627770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437627770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001437627770 none O=C(NCc1cc(Cl)ccc1I)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 16, 1, 1, 1, 18, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 11, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 121) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(NCc1cc(Cl)ccc1I)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001437627770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437627770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001437627770 none O=C(NCc1cc(Cl)ccc1I)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 16, 1, 1, 1, 18, 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] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 11, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437627770 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437627770 Building ZINC001437666713 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437666713 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/122 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc2c(c1NC(=O)[C@]([O-])([SiH3])c1cccc(C)c1)CN(C(=O)OC(C)(C)C)C2) `ZINC001437666713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437666713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001437666713 none COC(=O)c1sc2c(c1NC(=O)[C@]([O-])([SiH3])c1cccc(C)c1)CN(C(=O)OC(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 12, 17, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 6, 6, 2, 6, 6, 6, 12, 12, 12, 18, 18, 23, 23, 23, 23, 12, 17, 17, 17, 4, 6, 6, 2, 6, 6, 6, 6, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12] 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, 54]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/123 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1sc2c(c1NC(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)CN(C(=O)OC(C)(C)C)C2) `ZINC001437666713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437666713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001437666713 none COC(=O)c1sc2c(c1NC(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)CN(C(=O)OC(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 10, 13, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 10, 10, 10, 17, 17, 22, 22, 22, 22, 10, 13, 13, 13, 3, 6, 6, 2, 6, 6, 6, 6, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 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, 51, 52, 53, 54]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437666713 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713 Building ZINC001437666713 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437666713 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 122) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)c1sc2c(c1NC(=O)[C@]([O-])([SiH3])c1cccc(C)c1)CN(C(=O)OC(C)(C)C)C2) `ZINC001437666713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437666713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001437666713 none COC(=O)c1sc2c(c1NC(=O)[C@]([O-])([SiH3])c1cccc(C)c1)CN(C(=O)OC(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 12, 17, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 6, 6, 2, 6, 6, 6, 12, 12, 12, 18, 18, 23, 23, 23, 23, 12, 17, 17, 17, 4, 6, 6, 2, 6, 6, 6, 6, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12] 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, 54]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 123) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)c1sc2c(c1NC(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)CN(C(=O)OC(C)(C)C)C2) `ZINC001437666713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437666713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001437666713 none COC(=O)c1sc2c(c1NC(=O)[C@@]([O-])([SiH3])c1cccc(C)c1)CN(C(=O)OC(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 14, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 10, 13, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 10, 10, 10, 17, 17, 22, 22, 22, 22, 10, 13, 13, 13, 3, 6, 6, 2, 6, 6, 6, 6, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 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, 51, 52, 53, 54]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437666713 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437666713 Building ZINC001437733475 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437733475 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/124 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/124' -> `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)N1CCOC[C@H]1c1cc(F)cc(F)c1) `ZINC001437733475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437733475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001437733475 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1cc(F)cc(F)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 12, 12, 4, 4, 1, 1, 1, 2, 8, 9, 13, 13, 13, 13, 13, 13, 13, 28, 28, 28, 19, 28, 28, 28, 4, 4, 4, 12, 12, 7, 12, 12, 4, 4, 4, 13, 13, 13, 13, 13, 13, 28, 28, 28] 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: 113 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/125 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/125' -> `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)N1CCOC[C@H]1c1cc(F)cc(F)c1) `ZINC001437733475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437733475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001437733475 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1cc(F)cc(F)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 13, 13, 4, 4, 1, 1, 1, 1, 11, 11, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 21, 28, 28, 28, 4, 4, 4, 13, 13, 8, 13, 13, 4, 4, 4, 16, 16, 16, 16, 16, 16, 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, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437733475 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475 Building ZINC001437733475 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437733475 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 124) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1cc(F)cc(F)c1) `ZINC001437733475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437733475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001437733475 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1cc(F)cc(F)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 12, 12, 4, 4, 1, 1, 1, 2, 8, 9, 13, 13, 13, 13, 13, 13, 13, 28, 28, 28, 19, 28, 28, 28, 4, 4, 4, 12, 12, 7, 12, 12, 4, 4, 4, 13, 13, 13, 13, 13, 13, 28, 28, 28] 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: 113 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 125) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1cc(F)cc(F)c1) `ZINC001437733475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437733475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001437733475 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1cc(F)cc(F)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 13, 13, 4, 4, 1, 1, 1, 1, 11, 11, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 21, 28, 28, 28, 4, 4, 4, 13, 13, 8, 13, 13, 4, 4, 4, 16, 16, 16, 16, 16, 16, 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, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437733475 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733475 Building ZINC001437733476 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437733476 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/126 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/126' -> `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)N1CCOC[C@@H]1c1cc(F)cc(F)c1) `ZINC001437733476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437733476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001437733476 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1cc(F)cc(F)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 4, 4, 1, 1, 1, 2, 13, 14, 17, 17, 17, 17, 17, 17, 17, 29, 29, 29, 17, 29, 29, 29, 4, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 17, 17, 17, 17, 17, 17, 29, 17, 29] 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: 93 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/127 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/127' -> `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)N1CCOC[C@@H]1c1cc(F)cc(F)c1) `ZINC001437733476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437733476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001437733476 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1cc(F)cc(F)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 12, 15, 15, 15, 15, 15, 15, 15, 27, 27, 27, 15, 27, 27, 27, 4, 4, 4, 13, 13, 5, 13, 13, 4, 4, 4, 15, 15, 15, 15, 15, 15, 27, 15, 27] 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: 109 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437733476 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476 Building ZINC001437733476 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437733476 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 126) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1cc(F)cc(F)c1) `ZINC001437733476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437733476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001437733476 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1cc(F)cc(F)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 12, 4, 4, 1, 1, 1, 2, 13, 14, 17, 17, 17, 17, 17, 17, 17, 29, 29, 29, 17, 29, 29, 29, 4, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 17, 17, 17, 17, 17, 17, 29, 17, 29] 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: 93 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 127) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1cc(F)cc(F)c1) `ZINC001437733476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437733476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001437733476 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1cc(F)cc(F)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 12, 15, 15, 15, 15, 15, 15, 15, 27, 27, 27, 15, 27, 27, 27, 4, 4, 4, 13, 13, 5, 13, 13, 4, 4, 4, 15, 15, 15, 15, 15, 15, 27, 15, 27] 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: 109 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437733476 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437733476 Building ZINC001437789325 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437789325 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/128 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cnc1OC) `ZINC001437789325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437789325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001437789325 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cnc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 8, 1, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 8, 8, 8, 8, 8, 11, 11, 11, 8, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 8, 8, 8, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/129 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cnc1OC) `ZINC001437789325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437789325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001437789325 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cnc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 8, 1, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 6, 6, 6, 6, 6, 9, 9, 9, 6, 2, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437789325 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325 Building ZINC001437789325 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437789325 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 128) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cnc1OC) `ZINC001437789325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437789325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001437789325 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cnc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 8, 1, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 8, 8, 8, 8, 8, 11, 11, 11, 8, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 8, 8, 8, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 129) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cnc1OC) `ZINC001437789325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437789325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001437789325 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cnc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 8, 1, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7] 0 hydrogens 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, 6, 6, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 6, 6, 6, 6, 6, 9, 9, 9, 6, 2, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437789325 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437789325 Building ZINC001437837908 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437837908 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/130 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/130' -> `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]1CCCC[C@H]1NC(=O)c1ccccc1) `ZINC001437837908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437837908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001437837908 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)c1ccccc1 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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 8, 1, 11, 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, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 8, 18, 18, 18, 18, 18, 18, 18, 18, 28, 28, 28, 38, 38, 28, 38, 38, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 6, 18, 18, 18, 18, 18, 18, 18, 18, 28, 38, 38, 35, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 169 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/131 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/131' -> `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]1CCCC[C@H]1NC(=O)c1ccccc1) `ZINC001437837908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437837908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001437837908 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)c1ccccc1 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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 8, 1, 11, 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, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 6, 6, 8, 19, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 36, 36, 27, 36, 36, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 6, 19, 19, 19, 19, 19, 19, 19, 19, 27, 36, 36, 27, 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 154 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437837908 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908 Building ZINC001437837908 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437837908 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 130) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)c1ccccc1) `ZINC001437837908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437837908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001437837908 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)c1ccccc1 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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 8, 1, 11, 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, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 8, 18, 18, 18, 18, 18, 18, 18, 18, 28, 28, 28, 38, 38, 28, 38, 38, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 6, 18, 18, 18, 18, 18, 18, 18, 18, 28, 38, 38, 35, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 169 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 131) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/131: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)c1ccccc1) `ZINC001437837908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437837908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001437837908 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCC[C@H]1NC(=O)c1ccccc1 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', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 8, 1, 11, 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, 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, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 6, 6, 8, 19, 19, 19, 19, 19, 19, 19, 19, 27, 27, 27, 36, 36, 27, 36, 36, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 6, 19, 19, 19, 19, 19, 19, 19, 19, 27, 36, 36, 27, 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 154 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437837908 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437837908 Building ZINC001437955744 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437955744 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/132 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccc(I)cc2[nH]1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001437955744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437955744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001437955744 none O=C(Nc1nc2ccc(I)cc2[nH]1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 18, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 5, 5, 2, 5, 5, 5, 9, 10, 10, 10, 5, 5, 5, 5] 10 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]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/133 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc2ccc(I)cc2[nH]1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001437955744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437955744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001437955744 none O=C(Nc1nc2ccc(I)cc2[nH]1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 18, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 5, 5, 1, 1, 5, 5, 9, 10, 10, 10, 5, 5, 5, 5] 10 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]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437955744 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744 Building ZINC001437955744 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001437955744 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 132) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1nc2ccc(I)cc2[nH]1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001437955744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001437955744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001437955744 none O=C(Nc1nc2ccc(I)cc2[nH]1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 18, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 5, 5, 2, 5, 5, 5, 9, 10, 10, 10, 5, 5, 5, 5] 10 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]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 133) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1nc2ccc(I)cc2[nH]1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001437955744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001437955744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001437955744 none O=C(Nc1nc2ccc(I)cc2[nH]1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 18, 1, 1, 8, 6, 5, 12, 1, 1, 1, 1, 16, 1, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 5, 5, 1, 1, 5, 5, 9, 10, 10, 10, 5, 5, 5, 5] 10 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]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001437955744 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001437955744 Building ZINC001438116029 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438116029 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/134 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/134' -> `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)NCc1ccccc1C(=O)OC(C)(C)C) `ZINC001438116029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438116029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001438116029 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1C(=O)OC(C)(C)C 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 27, 27, 35, 36, 36, 36, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 8, 8, 8, 8, 8, 8, 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, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/135 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/135' -> `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)NCc1ccccc1C(=O)OC(C)(C)C) `ZINC001438116029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438116029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001438116029 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1C(=O)OC(C)(C)C 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 8, 8, 8, 8, 26, 26, 34, 34, 34, 34, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 8, 8, 8, 8, 8, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438116029 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029 Building ZINC001438116029 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438116029 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 134) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1C(=O)OC(C)(C)C) `ZINC001438116029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438116029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001438116029 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1C(=O)OC(C)(C)C 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 27, 27, 35, 36, 36, 36, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 8, 8, 8, 8, 8, 8, 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, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 135) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1C(=O)OC(C)(C)C) `ZINC001438116029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438116029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001438116029 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1C(=O)OC(C)(C)C 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 8, 8, 8, 8, 26, 26, 34, 34, 34, 34, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 8, 8, 8, 8, 8, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438116029 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438116029 Building ZINC001438340859 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001438340859 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/136 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1) `ZINC001438340859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438340859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001438340859 none COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 11, 18, 18, 11, 11, 11, 11, 11, 11, 17, 22, 22, 17, 22, 22, 11, 3, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 11, 11, 17, 17, 22, 22, 17, 22, 22, 11, 11, 1, 2, 2, 2, 2, 2, 2, 2, 18, 18] 50 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/137 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1) `ZINC001438340859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438340859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001438340859 none COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 12, 12, 12, 12, 12, 12, 22, 26, 26, 22, 26, 26, 12, 4, 12, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 12, 12, 22, 22, 26, 26, 22, 26, 26, 12, 12, 2, 4, 4, 4, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/138 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/138' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1) `ZINC001438340859.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001438340859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001438340859 none COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 11, 18, 18, 11, 11, 11, 11, 11, 11, 17, 22, 22, 17, 22, 22, 11, 3, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 11, 11, 17, 17, 22, 22, 17, 22, 22, 11, 11, 1, 2, 2, 2, 2, 2, 2, 2, 18, 18] 50 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/139 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/139' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1) `ZINC001438340859.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001438340859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001438340859 none COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 12, 12, 12, 12, 12, 12, 22, 26, 26, 22, 26, 26, 12, 4, 12, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 12, 12, 22, 22, 26, 26, 22, 26, 26, 12, 12, 2, 4, 4, 4, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438340859 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 Building ZINC001438340859 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001438340859 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 136) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1) `ZINC001438340859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438340859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001438340859 none COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 11, 18, 18, 11, 11, 11, 11, 11, 11, 17, 22, 22, 17, 22, 22, 11, 3, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 11, 11, 17, 17, 22, 22, 17, 22, 22, 11, 11, 1, 2, 2, 2, 2, 2, 2, 2, 18, 18] 50 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 137) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1) `ZINC001438340859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438340859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001438340859 none COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 12, 12, 12, 12, 12, 12, 22, 26, 26, 22, 26, 26, 12, 4, 12, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 12, 12, 22, 22, 26, 26, 22, 26, 26, 12, 12, 2, 4, 4, 4, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 138) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1) `ZINC001438340859.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001438340859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001438340859 none COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 11, 18, 18, 11, 11, 11, 11, 11, 11, 17, 22, 22, 17, 22, 22, 11, 3, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 11, 11, 17, 17, 22, 22, 17, 22, 22, 11, 11, 1, 2, 2, 2, 2, 2, 2, 2, 18, 18] 50 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 139) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1) `ZINC001438340859.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001438340859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001438340859 none COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 12, 12, 12, 12, 12, 12, 22, 26, 26, 22, 26, 26, 12, 4, 12, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 12, 12, 22, 22, 26, 26, 22, 26, 26, 12, 12, 2, 4, 4, 4, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438340859 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 Building ZINC001438340859 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001438340859 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 136) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1) `ZINC001438340859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438340859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001438340859 none COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 11, 18, 18, 11, 11, 11, 11, 11, 11, 17, 22, 22, 17, 22, 22, 11, 3, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 11, 11, 17, 17, 22, 22, 17, 22, 22, 11, 11, 1, 2, 2, 2, 2, 2, 2, 2, 18, 18] 50 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 137) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1) `ZINC001438340859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438340859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001438340859 none COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 12, 12, 12, 12, 12, 12, 22, 26, 26, 22, 26, 26, 12, 4, 12, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 12, 12, 22, 22, 26, 26, 22, 26, 26, 12, 12, 2, 4, 4, 4, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 138) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1) `ZINC001438340859.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001438340859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001438340859 none COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 11, 18, 18, 11, 11, 11, 11, 11, 11, 17, 22, 22, 17, 22, 22, 11, 3, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 11, 11, 17, 17, 22, 22, 17, 22, 22, 11, 11, 1, 2, 2, 2, 2, 2, 2, 2, 18, 18] 50 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 139) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1) `ZINC001438340859.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001438340859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001438340859 none COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 12, 12, 12, 12, 12, 12, 22, 26, 26, 22, 26, 26, 12, 4, 12, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 12, 12, 22, 22, 26, 26, 22, 26, 26, 12, 12, 2, 4, 4, 4, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438340859 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 Building ZINC001438340859 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001438340859 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 136) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1) `ZINC001438340859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438340859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001438340859 none COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 11, 18, 18, 11, 11, 11, 11, 11, 11, 17, 22, 22, 17, 22, 22, 11, 3, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 11, 11, 17, 17, 22, 22, 17, 22, 22, 11, 11, 1, 2, 2, 2, 2, 2, 2, 2, 18, 18] 50 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 137) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1) `ZINC001438340859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438340859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001438340859 none COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 12, 12, 12, 12, 12, 12, 22, 26, 26, 22, 26, 26, 12, 4, 12, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 12, 12, 22, 22, 26, 26, 22, 26, 26, 12, 12, 2, 4, 4, 4, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 138) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1) `ZINC001438340859.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001438340859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001438340859 none COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@]([O-])([SiH3])c2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 11, 18, 18, 11, 11, 11, 11, 11, 11, 17, 22, 22, 17, 22, 22, 11, 3, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 11, 11, 17, 17, 22, 22, 17, 22, 22, 11, 11, 1, 2, 2, 2, 2, 2, 2, 2, 18, 18] 50 rigid atoms, others: [50, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 139) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1) `ZINC001438340859.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001438340859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001438340859 none COc1ccc([C@@H]2CN(Cc3ccccc3)C[C@H]2NC(=O)[C@@]([O-])([SiH3])c2cccc(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 12, 12, 12, 12, 12, 12, 22, 26, 26, 22, 26, 26, 12, 4, 12, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 12, 12, 22, 22, 26, 26, 22, 26, 26, 12, 12, 2, 4, 4, 4, 4, 4, 4, 4, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438340859 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438340859 Building ZINC001438623991 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438623991 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/140 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](c1ccc(Br)s1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001438623991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438623991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001438623991 none COC(=O)[C@H](c1ccc(Br)s1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 17, 14, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 8, 13, 5, 8, 8, 17, 17, 17, 17, 17, 2, 5, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 17, 17, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/141 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](c1ccc(Br)s1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001438623991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438623991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001438623991 none COC(=O)[C@H](c1ccc(Br)s1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 17, 14, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 11, 18, 5, 11, 11, 20, 20, 20, 20, 20, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 18, 18, 18, 20, 20, 5, 5, 5, 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]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438623991 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991 Building ZINC001438623991 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438623991 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 140) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)[C@H](c1ccc(Br)s1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001438623991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438623991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001438623991 none COC(=O)[C@H](c1ccc(Br)s1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 17, 14, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 8, 13, 5, 8, 8, 17, 17, 17, 17, 17, 2, 5, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 17, 17, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 141) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)[C@H](c1ccc(Br)s1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001438623991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438623991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001438623991 none COC(=O)[C@H](c1ccc(Br)s1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 17, 14, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 11, 18, 5, 11, 11, 20, 20, 20, 20, 20, 2, 5, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 18, 18, 18, 20, 20, 5, 5, 5, 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]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438623991 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623991 Building ZINC001438623992 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438623992 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/142 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](c1ccc(Br)s1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001438623992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438623992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001438623992 none COC(=O)[C@@H](c1ccc(Br)s1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 17, 14, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 11, 18, 5, 11, 11, 20, 20, 20, 20, 20, 2, 5, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 20, 20, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/143 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/143' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](c1ccc(Br)s1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001438623992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438623992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001438623992 none COC(=O)[C@@H](c1ccc(Br)s1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 17, 14, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 8, 13, 5, 8, 8, 17, 17, 17, 17, 17, 2, 5, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 17, 17, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438623992 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992 Building ZINC001438623992 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438623992 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 142) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)[C@@H](c1ccc(Br)s1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001438623992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438623992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001438623992 none COC(=O)[C@@H](c1ccc(Br)s1)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 17, 14, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 11, 18, 5, 11, 11, 20, 20, 20, 20, 20, 2, 5, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 20, 20, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 143) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)[C@@H](c1ccc(Br)s1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001438623992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438623992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001438623992 none COC(=O)[C@@H](c1ccc(Br)s1)N(C)C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 1, 1, 1, 1, 17, 14, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 8, 13, 5, 8, 8, 17, 17, 17, 17, 17, 2, 5, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 17, 17, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438623992 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438623992 Building ZINC001438712925 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438712925 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/144 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/144' -> `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)Nc1ccc2c(c1)OCC(C)(C)C(=O)N2) `ZINC001438712925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438712925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001438712925 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCC(C)(C)C(=O)N2 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 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, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 15, 30, 30, 30, 15, 30, 30, 30, 30, 30, 30, 30, 30, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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, 50, 51, 52, 53, 54, 55]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/145 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/145' -> `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)Nc1ccc2c(c1)OCC(C)(C)C(=O)N2) `ZINC001438712925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438712925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001438712925 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCC(C)(C)C(=O)N2 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 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, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 15, 25, 25, 25, 15, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 3, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 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, 50, 51, 52, 53, 54, 55]) total number of confs: 118 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438712925 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925 Building ZINC001438712925 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438712925 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 144) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCC(C)(C)C(=O)N2) `ZINC001438712925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438712925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001438712925 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCC(C)(C)C(=O)N2 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 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, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 15, 30, 30, 30, 15, 30, 30, 30, 30, 30, 30, 30, 30, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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, 50, 51, 52, 53, 54, 55]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 145) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCC(C)(C)C(=O)N2) `ZINC001438712925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438712925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001438712925 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)OCC(C)(C)C(=O)N2 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 5, 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, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 15, 25, 25, 25, 15, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 3, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 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, 50, 51, 52, 53, 54, 55]) total number of confs: 118 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438712925 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438712925 Building ZINC001438745939 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001438745939 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/146 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2F)CC1) `ZINC001438745939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438745939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438745939 none CC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 14, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 3, 3, 8, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/147 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2F)CC1) `ZINC001438745939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438745939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438745939 none CC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 13, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 2, 2, 8, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/148 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/148' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2F)CC1) `ZINC001438745939.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001438745939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438745939 none CC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 14, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 3, 3, 8, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/149 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/149' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2F)CC1) `ZINC001438745939.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001438745939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438745939 none CC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 13, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 3, 3, 8, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438745939 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 Building ZINC001438745939 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001438745939 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 146) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2F)CC1) `ZINC001438745939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438745939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438745939 none CC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 14, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 3, 3, 8, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 147) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2F)CC1) `ZINC001438745939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438745939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438745939 none CC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 13, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 2, 2, 8, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 148) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2F)CC1) `ZINC001438745939.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001438745939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438745939 none CC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 14, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 3, 3, 8, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 149) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2F)CC1) `ZINC001438745939.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001438745939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438745939 none CC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 13, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 3, 3, 8, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438745939 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 Building ZINC001438745939 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001438745939 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 146) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2F)CC1) `ZINC001438745939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438745939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438745939 none CC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 14, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 3, 3, 8, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 147) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2F)CC1) `ZINC001438745939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438745939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438745939 none CC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 13, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 2, 2, 8, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 148) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2F)CC1) `ZINC001438745939.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001438745939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438745939 none CC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 14, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 3, 3, 8, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 149) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2F)CC1) `ZINC001438745939.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001438745939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438745939 none CC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 13, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 3, 3, 8, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438745939 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 Building ZINC001438745939 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001438745939 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 146) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2F)CC1) `ZINC001438745939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438745939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438745939 none CC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 14, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 3, 3, 8, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 147) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2F)CC1) `ZINC001438745939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438745939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438745939 none CC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)cc2F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 13, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 2, 2, 8, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 148) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2F)CC1) `ZINC001438745939.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001438745939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438745939 none CC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 14, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 3, 3, 8, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 75 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 149) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2F)CC1) `ZINC001438745939.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001438745939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001438745939 none CC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)cc2F)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 15, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 13, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 2, 3, 3, 8, 50, 50, 50, 50] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 74 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438745939 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438745939 Building ZINC001438863245 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438863245 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/150 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cc(Cl)cc(Br)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001438863245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438863245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001438863245 none O=C(NCCc1cc(Cl)cc(Br)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 15, 15, 28, 28, 28, 5, 5, 5, 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, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/151 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCc1cc(Cl)cc(Br)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001438863245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438863245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001438863245 none O=C(NCCc1cc(Cl)cc(Br)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 15, 15, 28, 28, 28, 5, 5, 5, 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, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438863245 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245 Building ZINC001438863245 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438863245 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 150) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCCc1cc(Cl)cc(Br)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001438863245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438863245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001438863245 none O=C(NCCc1cc(Cl)cc(Br)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 15, 15, 28, 28, 28, 5, 5, 5, 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, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 151) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCCc1cc(Cl)cc(Br)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001438863245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438863245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001438863245 none O=C(NCCc1cc(Cl)cc(Br)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 16, 1, 1, 17, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 9, 9, 15, 15, 28, 28, 28, 5, 5, 5, 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, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438863245 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438863245 Building ZINC001438884225 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438884225 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/152 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1) `ZINC001438884225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438884225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001438884225 none CCc1ccc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', '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', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 23, 23, 31, 31, 14, 5, 5, 5, 5, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 5, 5, 5, 5, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/153 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1ccc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1) `ZINC001438884225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438884225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001438884225 none CCc1ccc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', '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', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 33, 33, 13, 5, 5, 5, 5, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 5, 5, 5, 5, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 5, 5, 5, 5, 33, 33] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438884225 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225 Building ZINC001438884225 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438884225 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 152) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCc1ccc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1) `ZINC001438884225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438884225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001438884225 none CCc1ccc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', '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', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 23, 23, 31, 31, 14, 5, 5, 5, 5, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 5, 5, 5, 5, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 153) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCc1ccc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1) `ZINC001438884225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438884225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001438884225 none CCc1ccc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', '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', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 33, 33, 13, 5, 5, 5, 5, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 5, 5, 5, 5, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 5, 5, 5, 5, 33, 33] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438884225 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438884225 Building ZINC001438941090 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438941090 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/154 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc(c2noc(CC3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Cl)s4)CC3)n2)c1) `ZINC001438941090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438941090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001438941090 none Cc1ccnc(c2noc(CC3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Cl)s4)CC3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', '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', 'C.3', 'N.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, 1, 1, 1, 8, 1, 1, 8, 12, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 8, 1, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 37, 37, 37, 8, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 37, 47, 47, 47, 47, 47, 47, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 47] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/155 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccnc(c2noc(CC3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Cl)s4)CC3)n2)c1) `ZINC001438941090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438941090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001438941090 none Cc1ccnc(c2noc(CC3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Cl)s4)CC3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', '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', 'C.3', 'N.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, 1, 1, 1, 8, 1, 1, 8, 12, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 8, 1, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 6, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 26, 44, 44, 44, 44, 44, 44, 6, 6, 3, 3, 3, 3, 3, 2, 2, 3, 3, 3, 3, 44] 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438941090 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090 Building ZINC001438941090 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001438941090 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 154) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccnc(c2noc(CC3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Cl)s4)CC3)n2)c1) `ZINC001438941090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001438941090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001438941090 none Cc1ccnc(c2noc(CC3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Cl)s4)CC3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', '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', 'C.3', 'N.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, 1, 1, 1, 8, 1, 1, 8, 12, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 8, 1, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 37, 37, 37, 8, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 37, 47, 47, 47, 47, 47, 47, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 47] 50 rigid atoms, others: [17, 18, 19, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 155) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccnc(c2noc(CC3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Cl)s4)CC3)n2)c1) `ZINC001438941090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001438941090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001438941090 none Cc1ccnc(c2noc(CC3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Cl)s4)CC3)n2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', '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', 'C.3', 'N.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, 1, 1, 1, 8, 1, 1, 8, 12, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 8, 1, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 6, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 26, 44, 44, 44, 44, 44, 44, 6, 6, 3, 3, 3, 3, 3, 2, 2, 3, 3, 3, 3, 44] 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001438941090 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001438941090 Building ZINC001439211738 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439211738 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/156 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2cc(C(F)(F)F)ccc2Br)cn1) `ZINC001439211738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439211738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001439211738 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2cc(C(F)(F)F)ccc2Br)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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 1, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 6, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 33, 33, 33, 33, 33, 33, 23, 33, 33, 33, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 2, 14, 14, 33, 33, 33, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/157 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2cc(C(F)(F)F)ccc2Br)cn1) `ZINC001439211738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439211738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001439211738 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2cc(C(F)(F)F)ccc2Br)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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 1, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 6, 4, 4, 1, 1, 1, 1, 2, 2, 2, 14, 31, 31, 31, 31, 31, 31, 22, 31, 31, 31, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 2, 14, 14, 31, 31, 31, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439211738 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738 Building ZINC001439211738 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439211738 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 156) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2cc(C(F)(F)F)ccc2Br)cn1) `ZINC001439211738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439211738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001439211738 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2cc(C(F)(F)F)ccc2Br)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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 1, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 6, 6, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 33, 33, 33, 33, 33, 33, 23, 33, 33, 33, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 2, 14, 14, 33, 33, 33, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 157) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2cc(C(F)(F)F)ccc2Br)cn1) `ZINC001439211738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439211738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001439211738 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2cc(C(F)(F)F)ccc2Br)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.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 17, 1, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 6, 4, 4, 1, 1, 1, 1, 2, 2, 2, 14, 31, 31, 31, 31, 31, 31, 22, 31, 31, 31, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 2, 14, 14, 31, 31, 31, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439211738 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439211738 Building ZINC001439270644 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001439270644 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/158 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)cc1Cl) `ZINC001439270644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439270644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001439270644 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 1, 1, 16, 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, 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] 0 hydrogens 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, 3, 4, 4, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 17, 27, 27, 22, 27, 27, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 8, 8, 8, 4, 4, 2, 8, 8, 17, 17, 27, 27, 27, 27, 27, 8, 8, 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, 48, 49]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/159 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)cc1Cl) `ZINC001439270644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439270644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001439270644 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 1, 1, 16, 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, 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] 0 hydrogens 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, 4, 9, 9, 9, 9, 17, 25, 25, 21, 25, 25, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 17, 17, 25, 25, 25, 25, 25, 9, 9, 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, 48, 49]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/160 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/160' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)cc1Cl) `ZINC001439270644.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001439270644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001439270644 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 1, 1, 16, 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, 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] 0 hydrogens 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, 3, 4, 4, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 17, 27, 27, 22, 27, 27, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 8, 8, 8, 4, 4, 2, 8, 8, 17, 17, 27, 27, 27, 27, 27, 8, 8, 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, 48, 49]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/161 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/161' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)cc1Cl) `ZINC001439270644.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001439270644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001439270644 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 1, 1, 16, 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, 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] 0 hydrogens 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, 4, 9, 9, 9, 9, 17, 25, 25, 21, 25, 25, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 17, 17, 25, 25, 25, 25, 25, 9, 9, 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, 48, 49]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439270644 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 Building ZINC001439270644 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001439270644 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 158) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)cc1Cl) `ZINC001439270644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439270644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001439270644 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 1, 1, 16, 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, 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] 0 hydrogens 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, 3, 4, 4, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 17, 27, 27, 22, 27, 27, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 8, 8, 8, 4, 4, 2, 8, 8, 17, 17, 27, 27, 27, 27, 27, 8, 8, 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, 48, 49]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 159) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)cc1Cl) `ZINC001439270644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439270644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001439270644 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 1, 1, 16, 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, 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] 0 hydrogens 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, 4, 9, 9, 9, 9, 17, 25, 25, 21, 25, 25, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 17, 17, 25, 25, 25, 25, 25, 9, 9, 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, 48, 49]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 160) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)cc1Cl) `ZINC001439270644.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001439270644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001439270644 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 1, 1, 16, 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, 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] 0 hydrogens 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, 3, 4, 4, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 17, 27, 27, 22, 27, 27, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 8, 8, 8, 4, 4, 2, 8, 8, 17, 17, 27, 27, 27, 27, 27, 8, 8, 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, 48, 49]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 161) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)cc1Cl) `ZINC001439270644.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001439270644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001439270644 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 1, 1, 16, 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, 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] 0 hydrogens 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, 4, 9, 9, 9, 9, 17, 25, 25, 21, 25, 25, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 17, 17, 25, 25, 25, 25, 25, 9, 9, 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, 48, 49]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439270644 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 Building ZINC001439270644 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001439270644 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 158) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)cc1Cl) `ZINC001439270644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439270644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001439270644 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 1, 1, 16, 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, 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] 0 hydrogens 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, 3, 4, 4, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 17, 27, 27, 22, 27, 27, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 8, 8, 8, 4, 4, 2, 8, 8, 17, 17, 27, 27, 27, 27, 27, 8, 8, 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, 48, 49]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 159) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)cc1Cl) `ZINC001439270644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439270644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001439270644 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 1, 1, 16, 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, 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] 0 hydrogens 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, 4, 9, 9, 9, 9, 17, 25, 25, 21, 25, 25, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 17, 17, 25, 25, 25, 25, 25, 9, 9, 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, 48, 49]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 160) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)cc1Cl) `ZINC001439270644.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001439270644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001439270644 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 1, 1, 16, 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, 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] 0 hydrogens 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, 3, 4, 4, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 17, 27, 27, 22, 27, 27, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 8, 8, 8, 4, 4, 2, 8, 8, 17, 17, 27, 27, 27, 27, 27, 8, 8, 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, 48, 49]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 161) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)cc1Cl) `ZINC001439270644.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001439270644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001439270644 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 1, 1, 16, 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, 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] 0 hydrogens 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, 4, 9, 9, 9, 9, 17, 25, 25, 21, 25, 25, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 17, 17, 25, 25, 25, 25, 25, 9, 9, 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, 48, 49]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439270644 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 Building ZINC001439270644 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001439270644 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 158) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)cc1Cl) `ZINC001439270644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439270644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001439270644 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 1, 1, 16, 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, 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] 0 hydrogens 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, 3, 4, 4, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 17, 27, 27, 22, 27, 27, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 8, 8, 8, 4, 4, 2, 8, 8, 17, 17, 27, 27, 27, 27, 27, 8, 8, 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, 48, 49]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 159) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)cc1Cl) `ZINC001439270644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439270644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001439270644 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 1, 1, 16, 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, 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] 0 hydrogens 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, 4, 9, 9, 9, 9, 17, 25, 25, 21, 25, 25, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 17, 17, 25, 25, 25, 25, 25, 9, 9, 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, 48, 49]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 160) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)cc1Cl) `ZINC001439270644.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001439270644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001439270644 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 1, 1, 16, 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, 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] 0 hydrogens 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, 3, 4, 4, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 17, 27, 27, 22, 27, 27, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 8, 8, 8, 4, 4, 2, 8, 8, 17, 17, 27, 27, 27, 27, 27, 8, 8, 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, 48, 49]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 161) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)cc1Cl) `ZINC001439270644.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001439270644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001439270644 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(Cc3ccccc3)C[C@H]2C(F)(F)F)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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 1, 1, 16, 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, 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] 0 hydrogens 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, 4, 9, 9, 9, 9, 17, 25, 25, 21, 25, 25, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 8, 8, 8, 4, 4, 2, 9, 9, 17, 17, 25, 25, 25, 25, 25, 9, 9, 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, 48, 49]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439270644 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439270644 Building ZINC001439308243 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439308243 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/162 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(F)cc1F) `ZINC001439308243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439308243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001439308243 none CCOC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 15, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 9, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 12, 6, 6, 6, 3, 6, 6, 5, 6, 6, 6, 6, 19, 19, 19, 19, 19, 3, 3, 3, 6, 6, 12, 12, 12, 6, 6, 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, 46]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/163 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(F)cc1F) `ZINC001439308243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439308243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001439308243 none CCOC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 15, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 3, 8, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 2, 5, 10, 5, 5, 5, 3, 9, 9, 6, 9, 9, 9, 9, 15, 15, 15, 15, 15, 3, 3, 3, 5, 5, 10, 10, 10, 5, 9, 9, 9] 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: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439308243 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243 Building ZINC001439308243 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439308243 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 162) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(F)cc1F) `ZINC001439308243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439308243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001439308243 none CCOC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 15, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 9, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 12, 6, 6, 6, 3, 6, 6, 5, 6, 6, 6, 6, 19, 19, 19, 19, 19, 3, 3, 3, 6, 6, 12, 12, 12, 6, 6, 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, 46]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 163) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(F)cc1F) `ZINC001439308243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439308243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001439308243 none CCOC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(F)cc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', '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, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 15, 1, 1, 15, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 3, 8, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 2, 5, 10, 5, 5, 5, 3, 9, 9, 6, 9, 9, 9, 9, 15, 15, 15, 15, 15, 3, 3, 3, 5, 5, 10, 10, 10, 5, 9, 9, 9] 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: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439308243 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439308243 Building ZINC001439321741 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439321741 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/164 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(F)c(F)c1) `ZINC001439321741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439321741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001439321741 none CN1C(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 19, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 19, 19, 19, 45, 45, 45, 45, 45, 45, 45, 19, 19, 19, 19, 19, 4, 3, 1, 3, 45, 45, 45] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/165 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(F)c(F)c1) `ZINC001439321741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439321741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001439321741 none CN1C(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 18, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 18, 18, 44, 44, 44, 44, 44, 44, 44, 18, 18, 18, 18, 18, 3, 3, 1, 3, 44, 44, 44] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439321741 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741 Building ZINC001439321741 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439321741 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 164) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(F)c(F)c1) `ZINC001439321741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439321741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001439321741 none CN1C(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 19, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 19, 19, 19, 45, 45, 45, 45, 45, 45, 45, 19, 19, 19, 19, 19, 4, 3, 1, 3, 45, 45, 45] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 165) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(F)c(F)c1) `ZINC001439321741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439321741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001439321741 none CN1C(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)[C@H]1c1ccc(F)c(F)c1 NO_LONG_NAME dock atom types: ['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.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 1, 1, 1, 1, 15, 1, 15, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 18, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 18, 18, 44, 44, 44, 44, 44, 44, 44, 18, 18, 18, 18, 18, 3, 3, 1, 3, 44, 44, 44] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439321741 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439321741 Building ZINC001439338601 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439338601 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/166 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccnc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001439338601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439338601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001439338601 none CC(C)(C)OC(=O)Nc1ccnc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 39, 25, 39, 15, 15, 15, 15, 15, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 49, 49, 49, 49, 49, 49, 49, 49, 49, 25, 15, 15, 9, 9, 2, 3, 3, 15] 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/167 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccnc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001439338601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439338601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001439338601 none CC(C)(C)OC(=O)Nc1ccnc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 38, 25, 38, 15, 15, 15, 15, 15, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 49, 49, 49, 49, 49, 49, 49, 49, 49, 25, 15, 15, 9, 9, 2, 3, 3, 15] 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439338601 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601 Building ZINC001439338601 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439338601 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 166) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)Nc1ccnc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001439338601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439338601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001439338601 none CC(C)(C)OC(=O)Nc1ccnc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 39, 25, 39, 15, 15, 15, 15, 15, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 49, 49, 49, 49, 49, 49, 49, 49, 49, 25, 15, 15, 9, 9, 2, 3, 3, 15] 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]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 167) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)Nc1ccnc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1) `ZINC001439338601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439338601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001439338601 none CC(C)(C)OC(=O)Nc1ccnc(CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', '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, 5, 5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 38, 25, 38, 15, 15, 15, 15, 15, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 15, 49, 49, 49, 49, 49, 49, 49, 49, 49, 25, 15, 15, 9, 9, 2, 3, 3, 15] 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439338601 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439338601 Building ZINC001439562768 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439562768 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/168 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ncc(Br)cn2)CCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001439562768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439562768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001439562768 none O=C(NC1(c2ncc(Br)cn2)CCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 17, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 12, 21, 42, 42, 25, 42, 42, 42, 21, 21, 21, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 6, 42, 42, 21, 21, 21, 21, 21, 21, 6, 1, 6] 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/169 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ncc(Br)cn2)CCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001439562768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439562768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001439562768 none O=C(NC1(c2ncc(Br)cn2)CCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 17, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 12, 19, 41, 41, 27, 41, 41, 41, 19, 19, 19, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 6, 41, 41, 19, 19, 19, 19, 19, 19, 5, 1, 5] 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439562768 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768 Building ZINC001439562768 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439562768 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 168) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC1(c2ncc(Br)cn2)CCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001439562768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439562768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001439562768 none O=C(NC1(c2ncc(Br)cn2)CCC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 17, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 12, 21, 42, 42, 25, 42, 42, 42, 21, 21, 21, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 6, 42, 42, 21, 21, 21, 21, 21, 21, 6, 1, 6] 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 169) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC1(c2ncc(Br)cn2)CCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001439562768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439562768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001439562768 none O=C(NC1(c2ncc(Br)cn2)CCC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 17, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 12, 19, 41, 41, 27, 41, 41, 41, 19, 19, 19, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 6, 41, 41, 19, 19, 19, 19, 19, 19, 5, 1, 5] 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439562768 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439562768 Building ZINC001439580590 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439580590 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/170 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1CC1CC1) `ZINC001439580590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439580590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439580590 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1CC1CC1 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.3', 'F', 'F', 'F', 'C.ar', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 8, 8, 2, 2, 2, 20, 20, 2, 20, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/171 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1CC1CC1) `ZINC001439580590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439580590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439580590 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1CC1CC1 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.3', 'F', 'F', 'F', 'C.ar', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 12, 17, 17, 3, 3, 3, 19, 19, 4, 19, 3, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 113 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439580590 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590 Building ZINC001439580590 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439580590 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 170) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1CC1CC1) `ZINC001439580590.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439580590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439580590 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1CC1CC1 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.3', 'F', 'F', 'F', 'C.ar', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 8, 8, 2, 2, 2, 20, 20, 2, 20, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 171) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1CC1CC1) `ZINC001439580590.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439580590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439580590 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1CC1CC1 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.3', 'F', 'F', 'F', 'C.ar', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 19, 19, 3, 19, 19, 19, 19, 19, 19, 3, 3, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 12, 17, 17, 3, 3, 3, 19, 19, 4, 19, 3, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 17, 17, 17, 17, 17] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 113 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439580590 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580590 Building ZINC001439580610 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439580610 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/172 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1CC1CC1) `ZINC001439580610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439580610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439580610 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1CC1CC1 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.3', 'F', 'F', 'F', 'C.ar', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 4, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 12, 18, 18, 3, 3, 3, 24, 24, 5, 24, 3, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 125 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/173 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1CC1CC1) `ZINC001439580610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439580610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439580610 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1CC1CC1 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.3', 'F', 'F', 'F', 'C.ar', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 8, 8, 2, 2, 2, 20, 20, 2, 20, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439580610 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610 Building ZINC001439580610 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439580610 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 172) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1CC1CC1) `ZINC001439580610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439580610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439580610 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1CC1CC1 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.3', 'F', 'F', 'F', 'C.ar', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 4, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 5, 12, 18, 18, 3, 3, 3, 24, 24, 5, 24, 3, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 125 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 173) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1CC1CC1) `ZINC001439580610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439580610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439580610 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1CC1CC1 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.3', 'F', 'F', 'F', 'C.ar', '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', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 8, 8, 2, 2, 2, 20, 20, 2, 20, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 8, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439580610 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439580610 Building ZINC001439611239 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439611239 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/174 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1([C@@H]2CCCCO2)CC1) `ZINC001439611239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439611239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439611239 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1([C@@H]2CCCCO2)CC1 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.3', 'F', 'F', 'F', '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', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 6, 6, 6, 8, 15, 15, 15, 15, 15, 15, 8, 8, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 6, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/175 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1([C@@H]2CCCCO2)CC1) `ZINC001439611239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439611239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439611239 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1([C@@H]2CCCCO2)CC1 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.3', 'F', 'F', 'F', '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', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 7, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 6, 6, 6, 7, 13, 13, 13, 13, 13, 13, 6, 6, 2, 2, 2, 12, 12, 12, 12, 2, 2, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 64 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439611239 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239 Building ZINC001439611239 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439611239 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 174) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1([C@@H]2CCCCO2)CC1) `ZINC001439611239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439611239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439611239 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1([C@@H]2CCCCO2)CC1 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.3', 'F', 'F', 'F', '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', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 6, 6, 6, 8, 15, 15, 15, 15, 15, 15, 8, 8, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 6, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 175) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1([C@@H]2CCCCO2)CC1) `ZINC001439611239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439611239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439611239 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1([C@@H]2CCCCO2)CC1 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.3', 'F', 'F', 'F', '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', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 7, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 6, 6, 6, 7, 13, 13, 13, 13, 13, 13, 6, 6, 2, 2, 2, 12, 12, 12, 12, 2, 2, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 64 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439611239 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611239 Building ZINC001439611249 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439611249 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/176 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1([C@H]2CCCCO2)CC1) `ZINC001439611249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439611249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439611249 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1([C@H]2CCCCO2)CC1 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.3', 'F', 'F', 'F', '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', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 5, 5, 5, 6, 13, 13, 13, 13, 13, 13, 6, 6, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 5, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/177 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1([C@H]2CCCCO2)CC1) `ZINC001439611249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439611249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439611249 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1([C@H]2CCCCO2)CC1 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.3', 'F', 'F', 'F', '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', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 7, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 6, 6, 6, 8, 15, 15, 15, 15, 15, 15, 8, 8, 2, 2, 2, 12, 12, 7, 12, 2, 2, 2, 6, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439611249 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249 Building ZINC001439611249 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439611249 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 176) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1([C@H]2CCCCO2)CC1) `ZINC001439611249.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439611249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439611249 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1([C@H]2CCCCO2)CC1 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.3', 'F', 'F', 'F', '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', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 5, 5, 5, 6, 13, 13, 13, 13, 13, 13, 6, 6, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 5, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 177) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1([C@H]2CCCCO2)CC1) `ZINC001439611249.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439611249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439611249 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1([C@H]2CCCCO2)CC1 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.3', 'F', 'F', 'F', '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', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 12, 12, 7, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 6, 6, 6, 8, 15, 15, 15, 15, 15, 15, 8, 8, 2, 2, 2, 12, 12, 7, 12, 2, 2, 2, 6, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 62 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439611249 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439611249 Building ZINC001439647466 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439647466 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/178 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)c2cc(Br)ccc21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001439647466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439647466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001439647466 none O=C(N1CCNC(=O)c2cc(Br)ccc21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 2, 28, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 6, 1, 6] 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]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/179 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCNC(=O)c2cc(Br)ccc21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001439647466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439647466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001439647466 none O=C(N1CCNC(=O)c2cc(Br)ccc21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 2, 28, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 6, 1, 6] 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]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439647466 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466 Building ZINC001439647466 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439647466 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 178) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCNC(=O)c2cc(Br)ccc21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001439647466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439647466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001439647466 none O=C(N1CCNC(=O)c2cc(Br)ccc21)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 2, 28, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 6, 1, 6] 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]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 179) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCNC(=O)c2cc(Br)ccc21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001439647466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439647466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001439647466 none O=C(N1CCNC(=O)c2cc(Br)ccc21)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 2, 28, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 6, 1, 6] 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]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439647466 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439647466 Building ZINC001439958299 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439958299 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/180 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/180' -> `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](c1nccn1C)c1ccc(F)cc1F) `ZINC001439958299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439958299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001439958299 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1nccn1C)c1ccc(F)cc1F 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.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 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, 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] 0 hydrogens need 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, 10, 10, 5, 10, 10, 4, 4, 1, 1, 1, 1, 6, 6, 6, 12, 12, 24, 24, 24, 24, 24, 12, 25, 25, 15, 25, 25, 25, 25, 4, 4, 4, 10, 10, 6, 10, 10, 4, 4, 4, 6, 24, 24, 24, 24, 24, 25, 25, 25] 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, 50, 51, 52, 53]) total number of confs: 150 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/181 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/181' -> `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](c1nccn1C)c1ccc(F)cc1F) `ZINC001439958299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439958299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001439958299 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1nccn1C)c1ccc(F)cc1F 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.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 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, 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] 0 hydrogens need 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, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 6, 6, 6, 9, 9, 20, 20, 20, 20, 20, 9, 24, 24, 13, 24, 24, 24, 24, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 6, 20, 20, 20, 20, 20, 24, 24, 24] 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, 50, 51, 52, 53]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439958299 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299 Building ZINC001439958299 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439958299 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 180) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1nccn1C)c1ccc(F)cc1F) `ZINC001439958299.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439958299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001439958299 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1nccn1C)c1ccc(F)cc1F 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.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 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, 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] 0 hydrogens need 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, 10, 10, 5, 10, 10, 4, 4, 1, 1, 1, 1, 6, 6, 6, 12, 12, 24, 24, 24, 24, 24, 12, 25, 25, 15, 25, 25, 25, 25, 4, 4, 4, 10, 10, 6, 10, 10, 4, 4, 4, 6, 24, 24, 24, 24, 24, 25, 25, 25] 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, 50, 51, 52, 53]) total number of confs: 150 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 181) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1nccn1C)c1ccc(F)cc1F) `ZINC001439958299.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439958299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001439958299 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1nccn1C)c1ccc(F)cc1F 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.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 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, 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] 0 hydrogens need 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, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 6, 6, 6, 9, 9, 20, 20, 20, 20, 20, 9, 24, 24, 13, 24, 24, 24, 24, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 6, 20, 20, 20, 20, 20, 24, 24, 24] 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, 50, 51, 52, 53]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439958299 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958299 Building ZINC001439958305 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439958305 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/182 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/182' -> `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](c1nccn1C)c1ccc(F)cc1F) `ZINC001439958305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439958305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001439958305 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1nccn1C)c1ccc(F)cc1F 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.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 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, 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] 0 hydrogens need 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, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 6, 6, 6, 9, 9, 20, 20, 20, 20, 20, 9, 24, 24, 9, 24, 24, 24, 24, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 4, 6, 20, 20, 20, 20, 20, 24, 24, 24] 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, 50, 51, 52, 53]) total number of confs: 158 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/183 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/183' -> `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](c1nccn1C)c1ccc(F)cc1F) `ZINC001439958305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439958305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001439958305 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1nccn1C)c1ccc(F)cc1F 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.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 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, 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] 0 hydrogens need 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, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 6, 6, 6, 11, 11, 23, 23, 23, 23, 23, 11, 24, 24, 14, 24, 24, 24, 24, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 6, 23, 23, 23, 23, 23, 24, 24, 24] 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, 50, 51, 52, 53]) total number of confs: 150 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439958305 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305 Building ZINC001439958305 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439958305 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 182) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1nccn1C)c1ccc(F)cc1F) `ZINC001439958305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439958305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001439958305 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1nccn1C)c1ccc(F)cc1F 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.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 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, 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] 0 hydrogens need 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, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 6, 6, 6, 9, 9, 20, 20, 20, 20, 20, 9, 24, 24, 9, 24, 24, 24, 24, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 4, 6, 20, 20, 20, 20, 20, 24, 24, 24] 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, 50, 51, 52, 53]) total number of confs: 158 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 183) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1nccn1C)c1ccc(F)cc1F) `ZINC001439958305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439958305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001439958305 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1nccn1C)c1ccc(F)cc1F 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.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 15, 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, 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] 0 hydrogens need 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, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 6, 6, 6, 11, 11, 23, 23, 23, 23, 23, 11, 24, 24, 14, 24, 24, 24, 24, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 6, 23, 23, 23, 23, 23, 24, 24, 24] 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, 50, 51, 52, 53]) total number of confs: 150 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439958305 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439958305 Building ZINC001439963655 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439963655 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/184 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/184' -> `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](c1nccn1C)c1ccc(F)c(F)c1) `ZINC001439963655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439963655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001439963655 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1nccn1C)c1ccc(F)c(F)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', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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, 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] 0 hydrogens need 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, 6, 6, 3, 6, 6, 2, 2, 1, 1, 1, 1, 4, 4, 4, 6, 6, 18, 18, 18, 18, 18, 6, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 4, 18, 18, 18, 18, 18, 24, 24, 24] 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, 50, 51, 52, 53]) total number of confs: 74 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/185 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/185' -> `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](c1nccn1C)c1ccc(F)c(F)c1) `ZINC001439963655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439963655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001439963655 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1nccn1C)c1ccc(F)c(F)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', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 7, 7, 16, 16, 16, 16, 16, 7, 27, 27, 27, 27, 27, 27, 27, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 5, 16, 16, 16, 16, 16, 27, 27, 27] 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, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439963655 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655 Building ZINC001439963655 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439963655 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 184) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1nccn1C)c1ccc(F)c(F)c1) `ZINC001439963655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439963655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001439963655 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1nccn1C)c1ccc(F)c(F)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', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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, 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] 0 hydrogens need 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, 6, 6, 3, 6, 6, 2, 2, 1, 1, 1, 1, 4, 4, 4, 6, 6, 18, 18, 18, 18, 18, 6, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 2, 4, 18, 18, 18, 18, 18, 24, 24, 24] 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, 50, 51, 52, 53]) total number of confs: 74 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 185) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1nccn1C)c1ccc(F)c(F)c1) `ZINC001439963655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439963655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001439963655 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1nccn1C)c1ccc(F)c(F)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', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 7, 7, 16, 16, 16, 16, 16, 7, 27, 27, 27, 27, 27, 27, 27, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 5, 16, 16, 16, 16, 16, 27, 27, 27] 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, 50, 51, 52, 53]) total number of confs: 68 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439963655 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963655 Building ZINC001439963657 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439963657 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/186 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/186' -> `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](c1nccn1C)c1ccc(F)c(F)c1) `ZINC001439963657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439963657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001439963657 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1nccn1C)c1ccc(F)c(F)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', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 6, 6, 6, 8, 8, 17, 17, 17, 17, 17, 8, 27, 27, 27, 27, 27, 27, 27, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 6, 17, 17, 17, 17, 17, 27, 27, 27] 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, 50, 51, 52, 53]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/187 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/187' -> `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](c1nccn1C)c1ccc(F)c(F)c1) `ZINC001439963657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439963657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001439963657 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1nccn1C)c1ccc(F)c(F)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', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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, 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] 0 hydrogens need 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, 6, 6, 3, 6, 6, 2, 2, 1, 1, 1, 1, 5, 5, 5, 8, 8, 20, 20, 20, 20, 20, 8, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 2, 5, 20, 20, 20, 20, 20, 26, 26, 26] 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, 50, 51, 52, 53]) total number of confs: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439963657 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657 Building ZINC001439963657 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439963657 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 186) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1nccn1C)c1ccc(F)c(F)c1) `ZINC001439963657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439963657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001439963657 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1nccn1C)c1ccc(F)c(F)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', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 6, 6, 6, 8, 8, 17, 17, 17, 17, 17, 8, 27, 27, 27, 27, 27, 27, 27, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 6, 17, 17, 17, 17, 17, 27, 27, 27] 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, 50, 51, 52, 53]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 187) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1nccn1C)c1ccc(F)c(F)c1) `ZINC001439963657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439963657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001439963657 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1nccn1C)c1ccc(F)c(F)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', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 8, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 15, 1, 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, 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] 0 hydrogens need 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, 6, 6, 3, 6, 6, 2, 2, 1, 1, 1, 1, 5, 5, 5, 8, 8, 20, 20, 20, 20, 20, 8, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 2, 5, 20, 20, 20, 20, 20, 26, 26, 26] 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, 50, 51, 52, 53]) total number of confs: 84 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439963657 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439963657 Building ZINC001439969437 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439969437 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/188 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOC12CCCC2) `ZINC001439969437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439969437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439969437 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOC12CCCC2 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.3', 'F', 'F', 'F', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need 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, 9, 9, 4, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 9, 9, 8, 9, 2, 2, 2, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/189 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOC12CCCC2) `ZINC001439969437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439969437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439969437 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOC12CCCC2 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.3', 'F', 'F', 'F', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 8, 8, 5, 8, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439969437 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437 Building ZINC001439969437 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439969437 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 188) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOC12CCCC2) `ZINC001439969437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439969437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439969437 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCOC12CCCC2 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.3', 'F', 'F', 'F', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need 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, 9, 9, 4, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 9, 9, 8, 9, 2, 2, 2, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 189) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOC12CCCC2) `ZINC001439969437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439969437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439969437 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCOC12CCCC2 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.3', 'F', 'F', 'F', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 8, 8, 5, 8, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439969437 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969437 Building ZINC001439969441 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439969441 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/190 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOC12CCCC2) `ZINC001439969441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439969441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439969441 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOC12CCCC2 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.3', 'F', 'F', 'F', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 5, 8, 2, 2, 2, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/191 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOC12CCCC2) `ZINC001439969441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439969441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439969441 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOC12CCCC2 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.3', 'F', 'F', 'F', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 7, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 13, 13, 8, 13, 3, 3, 3, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439969441 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441 Building ZINC001439969441 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001439969441 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 190) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOC12CCCC2) `ZINC001439969441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001439969441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439969441 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOC12CCCC2 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.3', 'F', 'F', 'F', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 3, 3, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 5, 8, 2, 2, 2, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 191) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOC12CCCC2) `ZINC001439969441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001439969441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001439969441 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOC12CCCC2 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.3', 'F', 'F', 'F', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 7, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 13, 13, 8, 13, 3, 3, 3, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001439969441 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001439969441 Building ZINC001440048035 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001440048035 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/192 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440048035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048035 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 19, 26, 26, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 7, 7, 7, 7, 19, 19, 26, 26, 26, 26, 26, 7, 7, 7, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/193 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440048035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048035 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 8, 17, 26, 26, 26, 26, 26, 8, 8, 8, 8, 4, 4, 4, 10, 10, 10, 4, 4, 2, 8, 8, 8, 8, 8, 8, 17, 17, 26, 26, 26, 26, 26, 8, 8, 8, 8, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/194 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/194' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048035.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001440048035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048035 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 19, 26, 26, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 7, 7, 7, 7, 19, 19, 26, 26, 26, 26, 26, 7, 7, 7, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/195 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/195' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048035.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001440048035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048035 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 8, 17, 26, 26, 26, 26, 26, 8, 8, 8, 8, 4, 4, 4, 10, 10, 10, 4, 4, 2, 8, 8, 8, 8, 8, 8, 17, 17, 26, 26, 26, 26, 26, 8, 8, 8, 8, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440048035 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 Building ZINC001440048035 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001440048035 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 192) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440048035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048035 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 19, 26, 26, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 7, 7, 7, 7, 19, 19, 26, 26, 26, 26, 26, 7, 7, 7, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 193) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440048035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048035 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 8, 17, 26, 26, 26, 26, 26, 8, 8, 8, 8, 4, 4, 4, 10, 10, 10, 4, 4, 2, 8, 8, 8, 8, 8, 8, 17, 17, 26, 26, 26, 26, 26, 8, 8, 8, 8, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 194) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048035.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001440048035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048035 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 19, 26, 26, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 7, 7, 7, 7, 19, 19, 26, 26, 26, 26, 26, 7, 7, 7, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 195) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048035.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001440048035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048035 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 8, 17, 26, 26, 26, 26, 26, 8, 8, 8, 8, 4, 4, 4, 10, 10, 10, 4, 4, 2, 8, 8, 8, 8, 8, 8, 17, 17, 26, 26, 26, 26, 26, 8, 8, 8, 8, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440048035 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 Building ZINC001440048035 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001440048035 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 192) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440048035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048035 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 19, 26, 26, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 7, 7, 7, 7, 19, 19, 26, 26, 26, 26, 26, 7, 7, 7, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 193) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440048035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048035 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 8, 17, 26, 26, 26, 26, 26, 8, 8, 8, 8, 4, 4, 4, 10, 10, 10, 4, 4, 2, 8, 8, 8, 8, 8, 8, 17, 17, 26, 26, 26, 26, 26, 8, 8, 8, 8, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 194) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048035.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001440048035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048035 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 19, 26, 26, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 7, 7, 7, 7, 19, 19, 26, 26, 26, 26, 26, 7, 7, 7, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 195) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048035.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001440048035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048035 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 8, 17, 26, 26, 26, 26, 26, 8, 8, 8, 8, 4, 4, 4, 10, 10, 10, 4, 4, 2, 8, 8, 8, 8, 8, 8, 17, 17, 26, 26, 26, 26, 26, 8, 8, 8, 8, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440048035 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 Building ZINC001440048035 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001440048035 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 192) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440048035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048035 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 19, 26, 26, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 7, 7, 7, 7, 19, 19, 26, 26, 26, 26, 26, 7, 7, 7, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 193) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440048035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048035 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 8, 17, 26, 26, 26, 26, 26, 8, 8, 8, 8, 4, 4, 4, 10, 10, 10, 4, 4, 2, 8, 8, 8, 8, 8, 8, 17, 17, 26, 26, 26, 26, 26, 8, 8, 8, 8, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 194) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048035.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001440048035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048035 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 19, 26, 26, 26, 26, 26, 7, 7, 7, 7, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 7, 7, 7, 7, 19, 19, 26, 26, 26, 26, 26, 7, 7, 7, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 195) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048035.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001440048035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048035 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 8, 17, 26, 26, 26, 26, 26, 8, 8, 8, 8, 4, 4, 4, 10, 10, 10, 4, 4, 2, 8, 8, 8, 8, 8, 8, 17, 17, 26, 26, 26, 26, 26, 8, 8, 8, 8, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440048035 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048035 Building ZINC001440048036 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001440048036 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/196 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440048036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048036 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 18, 27, 27, 18, 27, 27, 7, 7, 7, 7, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 7, 7, 7, 7, 18, 18, 27, 27, 18, 27, 27, 7, 7, 7, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/197 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440048036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048036 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 16, 22, 22, 22, 22, 22, 6, 6, 6, 6, 5, 5, 5, 9, 9, 9, 5, 5, 2, 6, 6, 6, 6, 6, 6, 16, 16, 22, 22, 22, 22, 22, 6, 6, 6, 6, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/198 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/198' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048036.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001440048036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048036 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 18, 27, 27, 18, 27, 27, 7, 7, 7, 7, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 7, 7, 7, 7, 18, 18, 27, 27, 18, 27, 27, 7, 7, 7, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/199 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/199' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048036.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001440048036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048036 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 16, 22, 22, 22, 22, 22, 6, 6, 6, 6, 5, 5, 5, 9, 9, 9, 5, 5, 2, 6, 6, 6, 6, 6, 6, 16, 16, 22, 22, 22, 22, 22, 6, 6, 6, 6, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440048036 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 Building ZINC001440048036 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001440048036 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 196) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440048036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048036 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 18, 27, 27, 18, 27, 27, 7, 7, 7, 7, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 7, 7, 7, 7, 18, 18, 27, 27, 18, 27, 27, 7, 7, 7, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 197) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440048036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048036 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 16, 22, 22, 22, 22, 22, 6, 6, 6, 6, 5, 5, 5, 9, 9, 9, 5, 5, 2, 6, 6, 6, 6, 6, 6, 16, 16, 22, 22, 22, 22, 22, 6, 6, 6, 6, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 198) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048036.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001440048036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048036 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 18, 27, 27, 18, 27, 27, 7, 7, 7, 7, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 7, 7, 7, 7, 18, 18, 27, 27, 18, 27, 27, 7, 7, 7, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 199) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048036.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001440048036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048036 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 16, 22, 22, 22, 22, 22, 6, 6, 6, 6, 5, 5, 5, 9, 9, 9, 5, 5, 2, 6, 6, 6, 6, 6, 6, 16, 16, 22, 22, 22, 22, 22, 6, 6, 6, 6, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440048036 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 Building ZINC001440048036 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001440048036 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 196) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440048036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048036 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 18, 27, 27, 18, 27, 27, 7, 7, 7, 7, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 7, 7, 7, 7, 18, 18, 27, 27, 18, 27, 27, 7, 7, 7, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 197) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440048036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048036 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 16, 22, 22, 22, 22, 22, 6, 6, 6, 6, 5, 5, 5, 9, 9, 9, 5, 5, 2, 6, 6, 6, 6, 6, 6, 16, 16, 22, 22, 22, 22, 22, 6, 6, 6, 6, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 198) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048036.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001440048036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048036 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 18, 27, 27, 18, 27, 27, 7, 7, 7, 7, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 7, 7, 7, 7, 18, 18, 27, 27, 18, 27, 27, 7, 7, 7, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 199) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048036.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001440048036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048036 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 16, 22, 22, 22, 22, 22, 6, 6, 6, 6, 5, 5, 5, 9, 9, 9, 5, 5, 2, 6, 6, 6, 6, 6, 6, 16, 16, 22, 22, 22, 22, 22, 6, 6, 6, 6, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440048036 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 Building ZINC001440048036 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001440048036 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 196) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440048036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048036 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 18, 27, 27, 18, 27, 27, 7, 7, 7, 7, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 7, 7, 7, 7, 18, 18, 27, 27, 18, 27, 27, 7, 7, 7, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 197) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440048036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048036 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 16, 22, 22, 22, 22, 22, 6, 6, 6, 6, 5, 5, 5, 9, 9, 9, 5, 5, 2, 6, 6, 6, 6, 6, 6, 16, 16, 22, 22, 22, 22, 22, 6, 6, 6, 6, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 198) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048036.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001440048036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048036 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 7, 18, 27, 27, 18, 27, 27, 7, 7, 7, 7, 4, 4, 4, 10, 10, 10, 4, 4, 2, 7, 7, 7, 7, 7, 7, 18, 18, 27, 27, 18, 27, 27, 7, 7, 7, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 199) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)cc1Cl) `ZINC001440048036.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001440048036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440048036 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(Cc4ccccc4)C[C@@H]3C2)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', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 16, 22, 22, 22, 22, 22, 6, 6, 6, 6, 5, 5, 5, 9, 9, 9, 5, 5, 2, 6, 6, 6, 6, 6, 6, 16, 16, 22, 22, 22, 22, 22, 6, 6, 6, 6, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440048036 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440048036 Building ZINC001440093166 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440093166 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/200 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/200' -> `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)Nc1c(Br)cnn1C1CC1) `ZINC001440093166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440093166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001440093166 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cnn1C1CC1 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.2', 'C.2', 'Br', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 17, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 1, 1, 1, 1, 6, 6, 11, 19, 19, 19, 19, 19, 19, 31, 31, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 2, 11, 19, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/201 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/201' -> `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)Nc1c(Br)cnn1C1CC1) `ZINC001440093166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440093166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001440093166 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(Br)cnn1C1CC1 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.2', 'C.2', 'Br', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 17, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 9, 9, 2, 9, 9, 2, 2, 1, 1, 1, 1, 6, 6, 11, 19, 19, 19, 19, 19, 19, 34, 34, 2, 2, 2, 9, 9, 4, 9, 9, 2, 2, 2, 11, 19, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 128 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440093166 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166 Building ZINC001440093166 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440093166 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 200) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cnn1C1CC1) `ZINC001440093166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440093166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001440093166 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cnn1C1CC1 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.2', 'C.2', 'Br', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 17, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 1, 1, 1, 1, 6, 6, 11, 19, 19, 19, 19, 19, 19, 31, 31, 2, 2, 2, 8, 8, 2, 8, 8, 2, 2, 2, 11, 19, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 201) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(Br)cnn1C1CC1) `ZINC001440093166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440093166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001440093166 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(Br)cnn1C1CC1 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.2', 'C.2', 'Br', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 17, 1, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 9, 9, 2, 9, 9, 2, 2, 1, 1, 1, 1, 6, 6, 11, 19, 19, 19, 19, 19, 19, 34, 34, 2, 2, 2, 9, 9, 4, 9, 9, 2, 2, 2, 11, 19, 34, 34, 34, 34, 34] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 128 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440093166 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440093166 Building ZINC001440167054 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440167054 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/202 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC(OCc2ccc(Br)cc2)CC1) `ZINC001440167054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440167054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001440167054 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC(OCc2ccc(Br)cc2)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', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 17, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 8, 8, 8, 8, 18, 45, 49, 49, 46, 49, 49, 49, 8, 8, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 45, 45, 49, 49, 49, 49, 8, 8, 8, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 184 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/203 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC(OCc2ccc(Br)cc2)CC1) `ZINC001440167054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440167054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001440167054 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC(OCc2ccc(Br)cc2)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', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 17, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 5, 5, 5, 5, 15, 41, 49, 49, 45, 49, 49, 49, 5, 5, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 41, 41, 49, 49, 49, 49, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 179 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440167054 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054 Building ZINC001440167054 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440167054 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 202) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC(OCc2ccc(Br)cc2)CC1) `ZINC001440167054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440167054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001440167054 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC(OCc2ccc(Br)cc2)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', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 17, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 8, 8, 8, 8, 18, 45, 49, 49, 46, 49, 49, 49, 8, 8, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 45, 45, 49, 49, 49, 49, 8, 8, 8, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 184 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 203) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC(OCc2ccc(Br)cc2)CC1) `ZINC001440167054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440167054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001440167054 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC(OCc2ccc(Br)cc2)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', 'O.3', 'C.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', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 1, 1, 1, 17, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 2, 5, 5, 5, 5, 15, 41, 49, 49, 45, 49, 49, 49, 5, 5, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 41, 41, 49, 49, 49, 49, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 179 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440167054 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440167054 Building ZINC001440184767 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440184767 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/204 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(N(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC1) `ZINC001440184767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440184767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001440184767 none CC(C)(C)OC(=O)N1CCC(N(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 31, 14, 31, 14, 14, 12, 9, 3, 7, 9, 9, 9, 9, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 49, 49, 49, 49, 49, 49, 49, 49, 49, 14, 14, 14, 14, 14, 9, 9, 3, 3, 3, 3, 14, 14, 14, 14] 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, 53]) total number of confs: 152 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/205 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(N(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC1) `ZINC001440184767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440184767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001440184767 none CC(C)(C)OC(=O)N1CCC(N(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 13, 28, 13, 13, 13, 9, 3, 8, 10, 10, 10, 10, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 48, 48, 48, 48, 48, 48, 48, 48, 48, 13, 13, 13, 13, 13, 10, 10, 3, 3, 3, 3, 13, 13, 13, 13] 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, 53]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440184767 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767 Building ZINC001440184767 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440184767 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 204) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCC(N(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC1) `ZINC001440184767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440184767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001440184767 none CC(C)(C)OC(=O)N1CCC(N(CC(F)(F)F)C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 31, 14, 31, 14, 14, 12, 9, 3, 7, 9, 9, 9, 9, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 49, 49, 49, 49, 49, 49, 49, 49, 49, 14, 14, 14, 14, 14, 9, 9, 3, 3, 3, 3, 14, 14, 14, 14] 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, 53]) total number of confs: 152 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 205) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCC(N(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC1) `ZINC001440184767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440184767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001440184767 none CC(C)(C)OC(=O)N1CCC(N(CC(F)(F)F)C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 13, 28, 13, 13, 13, 9, 3, 8, 10, 10, 10, 10, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 48, 48, 48, 48, 48, 48, 48, 48, 48, 13, 13, 13, 13, 13, 10, 10, 3, 3, 3, 3, 13, 13, 13, 13] 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, 53]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440184767 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440184767 Building ZINC001440231487 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440231487 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/206 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1I) `ZINC001440231487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440231487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001440231487 none Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1I NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 18, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 16, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 23, 23, 11, 23, 23, 11, 16, 16, 16, 16, 16, 5, 16, 16, 5, 11, 23, 23, 11, 23, 23, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/207 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1I) `ZINC001440231487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440231487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001440231487 none Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1I NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 18, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 16, 16, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 23, 23, 11, 23, 23, 11, 16, 16, 16, 16, 16, 16, 16, 16, 5, 11, 23, 23, 23, 23, 23, 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440231487 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487 Building ZINC001440231487 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440231487 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 206) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1I) `ZINC001440231487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440231487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001440231487 none Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1I NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 18, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 16, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 23, 23, 11, 23, 23, 11, 16, 16, 16, 16, 16, 5, 16, 16, 5, 11, 23, 23, 11, 23, 23, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 207) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1I) `ZINC001440231487.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440231487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001440231487 none Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)c1I NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 18, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 16, 16, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 23, 23, 11, 23, 23, 11, 16, 16, 16, 16, 16, 16, 16, 16, 5, 11, 23, 23, 23, 23, 23, 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440231487 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440231487 Building ZINC001440372202 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440372202 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/208 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)N2CCCC2)c1) `ZINC001440372202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440372202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001440372202 none COc1cccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)N2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 10, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 38, 19, 12, 19, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 19, 23, 23, 23, 23, 38, 42, 42, 42, 38, 38, 38, 12, 12, 3, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 38] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/209 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)N2CCCC2)c1) `ZINC001440372202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440372202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001440372202 none COc1cccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)N2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 10, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 16, 12, 16, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 16, 20, 20, 20, 20, 32, 37, 37, 37, 32, 32, 32, 12, 12, 4, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440372202 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202 Building ZINC001440372202 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440372202 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 208) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1cccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)N2CCCC2)c1) `ZINC001440372202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440372202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001440372202 none COc1cccc([C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)N2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 10, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 38, 19, 12, 19, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 19, 23, 23, 23, 23, 38, 42, 42, 42, 38, 38, 38, 12, 12, 3, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 38] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 209) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1cccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)N2CCCC2)c1) `ZINC001440372202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440372202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001440372202 none COc1cccc([C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)N2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 10, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 16, 12, 16, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 16, 20, 20, 20, 20, 32, 37, 37, 37, 32, 32, 32, 12, 12, 4, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440372202 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372202 Building ZINC001440372204 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440372204 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/210 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)N2CCCC2)c1) `ZINC001440372204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440372204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001440372204 none COc1cccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)N2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 10, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 15, 12, 15, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 15, 20, 20, 20, 20, 31, 37, 37, 37, 31, 31, 31, 12, 12, 4, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 31] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/211 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)N2CCCC2)c1) `ZINC001440372204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440372204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001440372204 none COc1cccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)N2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 10, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 38, 19, 12, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 19, 23, 23, 23, 23, 38, 42, 42, 42, 38, 38, 38, 12, 12, 3, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 38] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440372204 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204 Building ZINC001440372204 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440372204 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 210) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1cccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)N2CCCC2)c1) `ZINC001440372204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440372204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001440372204 none COc1cccc([C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)N2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 10, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 15, 12, 15, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 15, 20, 20, 20, 20, 31, 37, 37, 37, 31, 31, 31, 12, 12, 4, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 31] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 211) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1cccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)N2CCCC2)c1) `ZINC001440372204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440372204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001440372204 none COc1cccc([C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)N2CCCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 10, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 38, 19, 12, 19, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 19, 23, 23, 23, 23, 38, 42, 42, 42, 38, 38, 38, 12, 12, 3, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 38] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440372204 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440372204 Building ZINC001440679292 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440679292 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/212 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)OCO2)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001440679292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440679292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001440679292 none O=C(Nc1ccc2c(c1)OCO2)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'Cl', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 3, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [41, 42, 43, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/213 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(c1)OCO2)C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001440679292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440679292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001440679292 none O=C(Nc1ccc2c(c1)OCO2)C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'Cl', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 3, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 16, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [41, 42, 43, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440679292 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292 Building ZINC001440679292 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440679292 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 212) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc2c(c1)OCO2)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001440679292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440679292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001440679292 none O=C(Nc1ccc2c(c1)OCO2)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'Cl', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 3, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [41, 42, 43, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 213) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc2c(c1)OCO2)C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001440679292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440679292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001440679292 none O=C(Nc1ccc2c(c1)OCO2)C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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', 'Cl', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 3, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 16, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [41, 42, 43, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440679292 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440679292 Building ZINC001440749851 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001440749851 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/214 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001440749851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440749851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440749851 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 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, 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] 0 hydrogens need 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, 1, 1, 1, 6, 5, 7, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 2, 2, 2, 2, 1, 2, 2, 1, 6, 6, 7, 7, 7, 7, 9, 9, 9, 9, 28, 28, 28, 28, 9, 9, 9, 9, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/215 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001440749851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440749851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440749851 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 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, 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] 0 hydrogens need 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, 1, 1, 1, 6, 6, 8, 11, 11, 11, 11, 29, 29, 13, 29, 29, 29, 29, 29, 29, 11, 11, 2, 2, 2, 2, 1, 2, 2, 1, 6, 6, 8, 8, 8, 8, 11, 11, 11, 11, 29, 29, 11, 29, 11, 11, 11, 11, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/216 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/216' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001440749851.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001440749851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440749851 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 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, 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] 0 hydrogens need 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, 1, 1, 1, 6, 5, 7, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 2, 2, 2, 2, 1, 2, 2, 1, 6, 6, 7, 7, 7, 7, 10, 10, 10, 10, 28, 28, 28, 28, 10, 10, 10, 10, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/217 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/217' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001440749851.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001440749851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440749851 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 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, 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] 0 hydrogens need 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, 1, 1, 1, 6, 6, 8, 11, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 2, 2, 2, 2, 1, 2, 2, 1, 6, 6, 8, 8, 8, 8, 11, 11, 11, 11, 29, 29, 29, 29, 11, 11, 11, 11, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440749851 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 Building ZINC001440749851 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001440749851 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 214) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001440749851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440749851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440749851 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 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, 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] 0 hydrogens need 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, 1, 1, 1, 6, 5, 7, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 2, 2, 2, 2, 1, 2, 2, 1, 6, 6, 7, 7, 7, 7, 9, 9, 9, 9, 28, 28, 28, 28, 9, 9, 9, 9, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 215) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001440749851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440749851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440749851 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 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, 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] 0 hydrogens need 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, 1, 1, 1, 6, 6, 8, 11, 11, 11, 11, 29, 29, 13, 29, 29, 29, 29, 29, 29, 11, 11, 2, 2, 2, 2, 1, 2, 2, 1, 6, 6, 8, 8, 8, 8, 11, 11, 11, 11, 29, 29, 11, 29, 11, 11, 11, 11, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 216) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001440749851.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001440749851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440749851 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 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, 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] 0 hydrogens need 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, 1, 1, 1, 6, 5, 7, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 2, 2, 2, 2, 1, 2, 2, 1, 6, 6, 7, 7, 7, 7, 10, 10, 10, 10, 28, 28, 28, 28, 10, 10, 10, 10, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 217) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001440749851.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001440749851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440749851 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 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, 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] 0 hydrogens need 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, 1, 1, 1, 6, 6, 8, 11, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 2, 2, 2, 2, 1, 2, 2, 1, 6, 6, 8, 8, 8, 8, 11, 11, 11, 11, 29, 29, 29, 29, 11, 11, 11, 11, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440749851 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 Building ZINC001440749851 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001440749851 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 214) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001440749851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440749851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440749851 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 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, 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] 0 hydrogens need 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, 1, 1, 1, 6, 5, 7, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 2, 2, 2, 2, 1, 2, 2, 1, 6, 6, 7, 7, 7, 7, 9, 9, 9, 9, 28, 28, 28, 28, 9, 9, 9, 9, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 215) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001440749851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440749851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440749851 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 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, 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] 0 hydrogens need 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, 1, 1, 1, 6, 6, 8, 11, 11, 11, 11, 29, 29, 13, 29, 29, 29, 29, 29, 29, 11, 11, 2, 2, 2, 2, 1, 2, 2, 1, 6, 6, 8, 8, 8, 8, 11, 11, 11, 11, 29, 29, 11, 29, 11, 11, 11, 11, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 216) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001440749851.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001440749851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440749851 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 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, 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] 0 hydrogens need 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, 1, 1, 1, 6, 5, 7, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 2, 2, 2, 2, 1, 2, 2, 1, 6, 6, 7, 7, 7, 7, 10, 10, 10, 10, 28, 28, 28, 28, 10, 10, 10, 10, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 217) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001440749851.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001440749851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440749851 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 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, 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] 0 hydrogens need 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, 1, 1, 1, 6, 6, 8, 11, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 2, 2, 2, 2, 1, 2, 2, 1, 6, 6, 8, 8, 8, 8, 11, 11, 11, 11, 29, 29, 29, 29, 11, 11, 11, 11, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440749851 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 Building ZINC001440749851 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001440749851 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 214) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001440749851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440749851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440749851 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 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, 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] 0 hydrogens need 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, 1, 1, 1, 6, 5, 7, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 2, 2, 2, 2, 1, 2, 2, 1, 6, 6, 7, 7, 7, 7, 9, 9, 9, 9, 28, 28, 28, 28, 9, 9, 9, 9, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 215) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001440749851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440749851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440749851 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 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, 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] 0 hydrogens need 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, 1, 1, 1, 6, 6, 8, 11, 11, 11, 11, 29, 29, 13, 29, 29, 29, 29, 29, 29, 11, 11, 2, 2, 2, 2, 1, 2, 2, 1, 6, 6, 8, 8, 8, 8, 11, 11, 11, 11, 29, 29, 11, 29, 11, 11, 11, 11, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 216) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001440749851.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001440749851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440749851 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 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, 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] 0 hydrogens need 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, 1, 1, 1, 6, 5, 7, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 2, 2, 2, 2, 1, 2, 2, 1, 6, 6, 7, 7, 7, 7, 10, 10, 10, 10, 28, 28, 28, 28, 10, 10, 10, 10, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 217) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001440749851.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001440749851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001440749851 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 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, 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] 0 hydrogens need 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, 1, 1, 1, 6, 6, 8, 11, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 11, 11, 2, 2, 2, 2, 1, 2, 2, 1, 6, 6, 8, 8, 8, 8, 11, 11, 11, 11, 29, 29, 29, 29, 11, 11, 11, 11, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440749851 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440749851 Building ZINC001440836582 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440836582 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/218 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001440836582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440836582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001440836582 none O=C(Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 6, 7, 12, 12, 12, 25, 32, 32, 29, 32, 32, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 25, 32, 32, 29, 32, 32, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/219 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001440836582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440836582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001440836582 none O=C(Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 13, 13, 13, 26, 32, 32, 28, 32, 32, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 26, 32, 32, 28, 32, 32, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440836582 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582 Building ZINC001440836582 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001440836582 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 218) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001440836582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001440836582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001440836582 none O=C(Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 6, 7, 12, 12, 12, 25, 32, 32, 29, 32, 32, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 25, 32, 32, 29, 32, 32, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 219) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001440836582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001440836582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001440836582 none O=C(Nc1ccc(S(=O)(=O)Nc2ccccc2)cc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 13, 13, 13, 26, 32, 32, 28, 32, 32, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 26, 32, 32, 28, 32, 32, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001440836582 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001440836582 Building ZINC001441015534 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001441015534 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/220 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC)c(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001441015534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441015534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001441015534 none COc1ccc(OC)c(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.3', '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', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 32, 40, 23, 9, 9, 9, 9, 4, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 32, 41, 41, 41, 32, 32, 40, 40, 40, 23, 23, 9, 9, 9, 9, 3, 1, 3, 9, 9, 9, 9, 32] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/221 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC)c(CN2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001441015534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441015534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001441015534 none COc1ccc(OC)c(CN2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.3', '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', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 35, 35, 35, 35, 35, 35, 48, 24, 9, 9, 9, 9, 4, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 35, 46, 46, 46, 35, 35, 48, 48, 48, 24, 24, 9, 9, 9, 9, 3, 1, 3, 9, 9, 9, 9, 35] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001441015534 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534 Building ZINC001441015534 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001441015534 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 220) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc(OC)c(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001441015534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441015534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001441015534 none COc1ccc(OC)c(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.3', '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', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 32, 40, 23, 9, 9, 9, 9, 4, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 32, 41, 41, 41, 32, 32, 40, 40, 40, 23, 23, 9, 9, 9, 9, 3, 1, 3, 9, 9, 9, 9, 32] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 221) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc(OC)c(CN2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001441015534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441015534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001441015534 none COc1ccc(OC)c(CN2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'N.3', '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', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 35, 35, 35, 35, 35, 35, 48, 24, 9, 9, 9, 9, 4, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 35, 46, 46, 46, 35, 35, 48, 48, 48, 24, 24, 9, 9, 9, 9, 3, 1, 3, 9, 9, 9, 9, 35] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001441015534 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441015534 Building ZINC001441315376 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001441315376 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/222 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001441315376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441315376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001441315376 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 7, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 6, 6, 6, 6, 7, 7, 9, 9, 9, 9, 27, 27, 27, 27, 9, 9, 9, 9, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/223 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001441315376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441315376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001441315376 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 6, 7, 8, 10, 10, 10, 10, 27, 27, 10, 27, 27, 27, 27, 27, 27, 10, 10, 4, 4, 4, 4, 2, 4, 4, 2, 5, 5, 7, 7, 7, 7, 8, 8, 10, 10, 10, 10, 27, 27, 27, 27, 10, 10, 10, 10, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/224 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/224' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001441315376.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001441315376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001441315376 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 7, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 6, 6, 6, 6, 7, 7, 9, 9, 9, 9, 27, 27, 27, 27, 9, 9, 9, 9, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/225 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/225' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001441315376.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001441315376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001441315376 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 6, 7, 8, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 4, 4, 4, 4, 2, 4, 4, 2, 5, 5, 7, 7, 7, 7, 8, 8, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 10, 10, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001441315376 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 Building ZINC001441315376 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001441315376 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 222) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001441315376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441315376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001441315376 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 7, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 6, 6, 6, 6, 7, 7, 9, 9, 9, 9, 27, 27, 27, 27, 9, 9, 9, 9, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 223) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001441315376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441315376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001441315376 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 6, 7, 8, 10, 10, 10, 10, 27, 27, 10, 27, 27, 27, 27, 27, 27, 10, 10, 4, 4, 4, 4, 2, 4, 4, 2, 5, 5, 7, 7, 7, 7, 8, 8, 10, 10, 10, 10, 27, 27, 27, 27, 10, 10, 10, 10, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 224) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001441315376.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001441315376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001441315376 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 7, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 6, 6, 6, 6, 7, 7, 9, 9, 9, 9, 27, 27, 27, 27, 9, 9, 9, 9, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 225) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001441315376.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001441315376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001441315376 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 6, 7, 8, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 4, 4, 4, 4, 2, 4, 4, 2, 5, 5, 7, 7, 7, 7, 8, 8, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 10, 10, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001441315376 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 Building ZINC001441315376 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001441315376 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 222) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001441315376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441315376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001441315376 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 7, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 6, 6, 6, 6, 7, 7, 9, 9, 9, 9, 27, 27, 27, 27, 9, 9, 9, 9, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 223) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001441315376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441315376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001441315376 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 6, 7, 8, 10, 10, 10, 10, 27, 27, 10, 27, 27, 27, 27, 27, 27, 10, 10, 4, 4, 4, 4, 2, 4, 4, 2, 5, 5, 7, 7, 7, 7, 8, 8, 10, 10, 10, 10, 27, 27, 27, 27, 10, 10, 10, 10, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 224) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001441315376.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001441315376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001441315376 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 7, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 6, 6, 6, 6, 7, 7, 9, 9, 9, 9, 27, 27, 27, 27, 9, 9, 9, 9, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 225) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001441315376.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001441315376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001441315376 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 6, 7, 8, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 4, 4, 4, 4, 2, 4, 4, 2, 5, 5, 7, 7, 7, 7, 8, 8, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 10, 10, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001441315376 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 Building ZINC001441315376 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001441315376 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 222) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001441315376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441315376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001441315376 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 7, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 6, 6, 6, 6, 7, 7, 9, 9, 9, 9, 27, 27, 27, 27, 9, 9, 9, 9, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 223) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001441315376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441315376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001441315376 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 6, 7, 8, 10, 10, 10, 10, 27, 27, 10, 27, 27, 27, 27, 27, 27, 10, 10, 4, 4, 4, 4, 2, 4, 4, 2, 5, 5, 7, 7, 7, 7, 8, 8, 10, 10, 10, 10, 27, 27, 27, 27, 10, 10, 10, 10, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 224) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001441315376.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001441315376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001441315376 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 5, 6, 7, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 6, 6, 6, 6, 7, 7, 9, 9, 9, 9, 27, 27, 27, 27, 9, 9, 9, 9, 2] 50 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 225) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1) `ZINC001441315376.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001441315376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001441315376 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCCCC[N@]2CC[N@@](c3cccc(C(F)(F)F)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 6, 7, 8, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 4, 4, 4, 4, 2, 4, 4, 2, 5, 5, 7, 7, 7, 7, 8, 8, 10, 10, 10, 10, 26, 26, 26, 26, 10, 10, 10, 10, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001441315376 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441315376 Building ZINC001441693490 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001441693490 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/226 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCC[N@]1CC[N@](Cc2ccccc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441693490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441693490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001441693490 none O=C(NCCCC[N@]1CC[N@](Cc2ccccc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 18, 24, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 18, 18, 18, 18, 24, 24, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/227 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCC[N@]1CC[N@@](Cc2ccccc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441693490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441693490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001441693490 none O=C(NCCCC[N@]1CC[N@@](Cc2ccccc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 18, 24, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 18, 18, 18, 18, 24, 24, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/228 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/228' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCC[N@]1CC[N@](Cc2ccccc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441693490.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001441693490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001441693490 none O=C(NCCCC[N@]1CC[N@](Cc2ccccc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 17, 23, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 17, 17, 17, 17, 23, 23, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/229 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/229' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCC[N@]1CC[N@@](Cc2ccccc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441693490.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001441693490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001441693490 none O=C(NCCCC[N@]1CC[N@@](Cc2ccccc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 17, 23, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 17, 17, 17, 17, 23, 23, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001441693490 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 Building ZINC001441693490 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001441693490 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 226) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCCCC[N@]1CC[N@](Cc2ccccc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441693490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441693490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001441693490 none O=C(NCCCC[N@]1CC[N@](Cc2ccccc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 18, 24, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 18, 18, 18, 18, 24, 24, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 227) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCCCC[N@]1CC[N@@](Cc2ccccc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441693490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441693490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001441693490 none O=C(NCCCC[N@]1CC[N@@](Cc2ccccc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 18, 24, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 18, 18, 18, 18, 24, 24, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 228) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NCCCC[N@]1CC[N@](Cc2ccccc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441693490.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001441693490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001441693490 none O=C(NCCCC[N@]1CC[N@](Cc2ccccc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 17, 23, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 17, 17, 17, 17, 23, 23, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 229) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NCCCC[N@]1CC[N@@](Cc2ccccc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441693490.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001441693490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001441693490 none O=C(NCCCC[N@]1CC[N@@](Cc2ccccc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 17, 23, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 17, 17, 17, 17, 23, 23, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001441693490 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 Building ZINC001441693490 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001441693490 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 226) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCCCC[N@]1CC[N@](Cc2ccccc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441693490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441693490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001441693490 none O=C(NCCCC[N@]1CC[N@](Cc2ccccc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 18, 24, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 18, 18, 18, 18, 24, 24, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 227) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCCCC[N@]1CC[N@@](Cc2ccccc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441693490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441693490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001441693490 none O=C(NCCCC[N@]1CC[N@@](Cc2ccccc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 18, 24, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 18, 18, 18, 18, 24, 24, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 228) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NCCCC[N@]1CC[N@](Cc2ccccc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441693490.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001441693490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001441693490 none O=C(NCCCC[N@]1CC[N@](Cc2ccccc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 17, 23, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 17, 17, 17, 17, 23, 23, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 229) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NCCCC[N@]1CC[N@@](Cc2ccccc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441693490.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001441693490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001441693490 none O=C(NCCCC[N@]1CC[N@@](Cc2ccccc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 17, 23, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 17, 17, 17, 17, 23, 23, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001441693490 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 Building ZINC001441693490 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001441693490 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 226) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCCCC[N@]1CC[N@](Cc2ccccc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441693490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001441693490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001441693490 none O=C(NCCCC[N@]1CC[N@](Cc2ccccc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 18, 24, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 18, 18, 18, 18, 24, 24, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 227) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCCCC[N@]1CC[N@@](Cc2ccccc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441693490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001441693490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001441693490 none O=C(NCCCC[N@]1CC[N@@](Cc2ccccc2)CC1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 18, 24, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 18, 18, 18, 18, 24, 24, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 228) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NCCCC[N@]1CC[N@](Cc2ccccc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441693490.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001441693490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001441693490 none O=C(NCCCC[N@]1CC[N@](Cc2ccccc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 17, 23, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 17, 17, 17, 17, 23, 23, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 229) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NCCCC[N@]1CC[N@@](Cc2ccccc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001441693490.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001441693490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001441693490 none O=C(NCCCC[N@]1CC[N@@](Cc2ccccc2)CC1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 17, 23, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 9, 9, 17, 17, 17, 17, 23, 23, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 2, 1, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001441693490 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001441693490 Building ZINC001442401267 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442401267 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/230 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1nc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cs1) `ZINC001442401267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442401267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001442401267 none CC(C)(C)c1nc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 36, 36, 34, 34, 15, 6, 6, 6, 6, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 34, 34, 36, 36, 36, 36, 36, 36, 36, 36, 36, 15, 15, 6, 6, 6, 6, 4, 4, 4, 4, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/231 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1nc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cs1) `ZINC001442401267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442401267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001442401267 none CC(C)(C)c1nc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 33, 33, 32, 32, 13, 5, 5, 5, 5, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 32, 32, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 5, 5, 5, 5, 4, 4, 4, 4, 5, 5, 5, 5, 32] 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442401267 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267 Building ZINC001442401267 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442401267 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 230) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)c1nc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cs1) `ZINC001442401267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442401267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001442401267 none CC(C)(C)c1nc(CN2CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 36, 36, 34, 34, 15, 6, 6, 6, 6, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 34, 34, 36, 36, 36, 36, 36, 36, 36, 36, 36, 15, 15, 6, 6, 6, 6, 4, 4, 4, 4, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 231) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)c1nc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cs1) `ZINC001442401267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442401267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001442401267 none CC(C)(C)c1nc(CN2CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)CC2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 33, 33, 32, 32, 13, 5, 5, 5, 5, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 32, 32, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 5, 5, 5, 5, 4, 4, 4, 4, 5, 5, 5, 5, 32] 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442401267 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442401267 Building ZINC001442470940 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442470940 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/232 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncn(Cc2cccc(Br)c2)n1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001442470940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442470940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001442470940 none O=C(Nc1ncn(Cc2cccc(Br)c2)n1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 8, 10, 11, 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, 1, 3, 3, 4, 4, 4, 4, 14, 31, 31, 26, 31, 31, 31, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 14, 14, 31, 31, 31, 31, 4, 4, 4, 4] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/233 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncn(Cc2cccc(Br)c2)n1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001442470940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442470940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001442470940 none O=C(Nc1ncn(Cc2cccc(Br)c2)n1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 8, 10, 11, 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, 1, 3, 3, 4, 4, 4, 4, 14, 30, 30, 30, 30, 30, 30, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 14, 14, 30, 30, 30, 30, 4, 4, 4, 4] 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442470940 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940 Building ZINC001442470940 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442470940 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 232) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ncn(Cc2cccc(Br)c2)n1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001442470940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442470940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001442470940 none O=C(Nc1ncn(Cc2cccc(Br)c2)n1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 8, 10, 11, 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, 1, 3, 3, 4, 4, 4, 4, 14, 31, 31, 26, 31, 31, 31, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 14, 14, 31, 31, 31, 31, 4, 4, 4, 4] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 233) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ncn(Cc2cccc(Br)c2)n1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001442470940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442470940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001442470940 none O=C(Nc1ncn(Cc2cccc(Br)c2)n1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 8, 10, 11, 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, 1, 3, 3, 4, 4, 4, 4, 14, 30, 30, 30, 30, 30, 30, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 14, 14, 30, 30, 30, 30, 4, 4, 4, 4] 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442470940 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442470940 Building ZINC001442534532 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001442534532 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/234 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442534532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534532 none O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [2, 1, 2, 2, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 2, 14, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/235 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442534532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534532 none O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [2, 1, 2, 2, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 2, 14, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/236 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/236' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534532.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001442534532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534532 none O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 24, 41, 41, 41, 41, 41, 42, 42, 41, 41, 42, 42, 41, 1, 1, 1, 7, 7, 7, 7, 7, 3, 13, 13, 41, 41, 41, 41, 42, 42, 42, 42, 41, 41, 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/237 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/237' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534532.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001442534532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534532 none O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 24, 41, 41, 41, 41, 41, 42, 42, 41, 41, 42, 42, 41, 1, 1, 1, 7, 7, 7, 7, 7, 3, 13, 13, 41, 41, 41, 41, 42, 42, 42, 42, 41, 41, 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442534532 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 Building ZINC001442534532 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001442534532 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 234) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442534532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534532 none O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [2, 1, 2, 2, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 2, 14, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 235) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442534532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534532 none O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [2, 1, 2, 2, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 2, 14, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 236) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534532.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001442534532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534532 none O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 24, 41, 41, 41, 41, 41, 42, 42, 41, 41, 42, 42, 41, 1, 1, 1, 7, 7, 7, 7, 7, 3, 13, 13, 41, 41, 41, 41, 42, 42, 42, 42, 41, 41, 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 237) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534532.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001442534532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534532 none O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 24, 41, 41, 41, 41, 41, 42, 42, 41, 41, 42, 42, 41, 1, 1, 1, 7, 7, 7, 7, 7, 3, 13, 13, 41, 41, 41, 41, 42, 42, 42, 42, 41, 41, 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442534532 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 Building ZINC001442534532 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001442534532 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 234) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442534532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534532 none O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [2, 1, 2, 2, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 2, 14, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 235) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442534532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534532 none O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [2, 1, 2, 2, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 2, 14, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 236) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534532.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001442534532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534532 none O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 24, 41, 41, 41, 41, 41, 42, 42, 41, 41, 42, 42, 41, 1, 1, 1, 7, 7, 7, 7, 7, 3, 13, 13, 41, 41, 41, 41, 42, 42, 42, 42, 41, 41, 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 237) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534532.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001442534532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534532 none O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 24, 41, 41, 41, 41, 41, 42, 42, 41, 41, 42, 42, 41, 1, 1, 1, 7, 7, 7, 7, 7, 3, 13, 13, 41, 41, 41, 41, 42, 42, 42, 42, 41, 41, 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442534532 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 Building ZINC001442534532 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001442534532 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 234) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442534532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534532 none O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [2, 1, 2, 2, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 2, 14, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 235) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442534532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534532 none O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [2, 1, 2, 2, 22, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 2, 14, 14, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5] 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 236) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534532.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001442534532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534532 none O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 24, 41, 41, 41, 41, 41, 42, 42, 41, 41, 42, 42, 41, 1, 1, 1, 7, 7, 7, 7, 7, 3, 13, 13, 41, 41, 41, 41, 42, 42, 42, 42, 41, 41, 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 237) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534532.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001442534532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534532 none O=C(NC[C@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 24, 41, 41, 41, 41, 41, 42, 42, 41, 41, 42, 42, 41, 1, 1, 1, 7, 7, 7, 7, 7, 3, 13, 13, 41, 41, 41, 41, 42, 42, 42, 42, 41, 41, 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442534532 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534532 Building ZINC001442534542 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001442534542 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/238 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442534542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534542 none O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 23, 40, 40, 40, 40, 40, 41, 41, 40, 40, 41, 41, 40, 1, 1, 1, 7, 7, 7, 7, 7, 3, 13, 13, 40, 40, 40, 40, 41, 41, 41, 41, 40, 40, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/239 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442534542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534542 none O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 23, 40, 40, 40, 40, 40, 41, 41, 40, 40, 41, 41, 40, 1, 1, 1, 7, 7, 7, 7, 7, 3, 13, 13, 40, 40, 40, 40, 41, 41, 41, 41, 40, 40, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/240 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/240' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534542.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001442534542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534542 none O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [2, 1, 2, 2, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 2, 13, 13, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/241 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/241' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534542.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001442534542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534542 none O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [2, 1, 2, 2, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 2, 13, 13, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442534542 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 Building ZINC001442534542 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001442534542 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 238) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442534542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534542 none O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 23, 40, 40, 40, 40, 40, 41, 41, 40, 40, 41, 41, 40, 1, 1, 1, 7, 7, 7, 7, 7, 3, 13, 13, 40, 40, 40, 40, 41, 41, 41, 41, 40, 40, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 239) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442534542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534542 none O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 23, 40, 40, 40, 40, 40, 41, 41, 40, 40, 41, 41, 40, 1, 1, 1, 7, 7, 7, 7, 7, 3, 13, 13, 40, 40, 40, 40, 41, 41, 41, 41, 40, 40, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 240) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534542.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001442534542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534542 none O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [2, 1, 2, 2, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 2, 13, 13, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 241) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534542.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001442534542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534542 none O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [2, 1, 2, 2, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 2, 13, 13, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442534542 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 Building ZINC001442534542 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001442534542 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 238) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442534542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534542 none O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 23, 40, 40, 40, 40, 40, 41, 41, 40, 40, 41, 41, 40, 1, 1, 1, 7, 7, 7, 7, 7, 3, 13, 13, 40, 40, 40, 40, 41, 41, 41, 41, 40, 40, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 239) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442534542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534542 none O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 23, 40, 40, 40, 40, 40, 41, 41, 40, 40, 41, 41, 40, 1, 1, 1, 7, 7, 7, 7, 7, 3, 13, 13, 40, 40, 40, 40, 41, 41, 41, 41, 40, 40, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 240) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534542.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001442534542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534542 none O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [2, 1, 2, 2, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 2, 13, 13, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 241) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534542.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001442534542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534542 none O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [2, 1, 2, 2, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 2, 13, 13, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442534542 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 Building ZINC001442534542 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001442534542 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 238) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442534542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534542 none O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 23, 40, 40, 40, 40, 40, 41, 41, 40, 40, 41, 41, 40, 1, 1, 1, 7, 7, 7, 7, 7, 3, 13, 13, 40, 40, 40, 40, 41, 41, 41, 41, 40, 40, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 239) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442534542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534542 none O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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, 23, 40, 40, 40, 40, 40, 41, 41, 40, 40, 41, 41, 40, 1, 1, 1, 7, 7, 7, 7, 7, 3, 13, 13, 40, 40, 40, 40, 41, 41, 41, 41, 40, 40, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 240) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534542.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001442534542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534542 none O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [2, 1, 2, 2, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 2, 13, 13, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 241) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001442534542.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001442534542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001442534542 none O=C(NC[C@@H]1CCN(c2ccc(Cl)cc2)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', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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: [2, 1, 2, 2, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 1, 5, 5, 5, 5, 5, 2, 13, 13, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442534542 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442534542 Building ZINC001442669932 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442669932 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/242 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](c2ccccc2Br)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001442669932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442669932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001442669932 none O=C(N1CCO[C@@H](c2ccccc2Br)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 12, 12, 12, 12, 12, 12, 28, 28, 12, 28, 28, 28, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 28, 28, 18, 28, 12, 12, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/243 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](c2ccccc2Br)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001442669932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442669932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001442669932 none O=C(N1CCO[C@@H](c2ccccc2Br)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 11, 11, 11, 11, 11, 11, 24, 24, 17, 24, 24, 24, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 24, 24, 23, 24, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442669932 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932 Building ZINC001442669932 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442669932 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 242) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(N1CCO[C@@H](c2ccccc2Br)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001442669932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442669932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001442669932 none O=C(N1CCO[C@@H](c2ccccc2Br)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 12, 12, 12, 12, 12, 12, 28, 28, 12, 28, 28, 28, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 28, 28, 18, 28, 12, 12, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 243) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(N1CCO[C@@H](c2ccccc2Br)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001442669932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442669932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001442669932 none O=C(N1CCO[C@@H](c2ccccc2Br)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 11, 11, 11, 11, 11, 11, 24, 24, 17, 24, 24, 24, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 24, 24, 23, 24, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442669932 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669932 Building ZINC001442669940 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442669940 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/244 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](c2ccccc2Br)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001442669940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442669940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001442669940 none O=C(N1CCO[C@H](c2ccccc2Br)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 11, 11, 11, 11, 11, 11, 25, 25, 14, 25, 25, 25, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 25, 25, 17, 25, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/245 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@H](c2ccccc2Br)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001442669940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442669940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001442669940 none O=C(N1CCO[C@H](c2ccccc2Br)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 12, 12, 12, 12, 12, 12, 29, 29, 14, 29, 29, 29, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 29, 29, 18, 29, 12, 12, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442669940 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940 Building ZINC001442669940 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442669940 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 244) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(N1CCO[C@H](c2ccccc2Br)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001442669940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442669940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001442669940 none O=C(N1CCO[C@H](c2ccccc2Br)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 11, 11, 11, 11, 11, 11, 25, 25, 14, 25, 25, 25, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 25, 25, 17, 25, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 245) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(N1CCO[C@H](c2ccccc2Br)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001442669940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442669940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001442669940 none O=C(N1CCO[C@H](c2ccccc2Br)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 1, 1, 17, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 6, 12, 12, 12, 12, 12, 12, 29, 29, 14, 29, 29, 29, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 29, 29, 18, 29, 12, 12, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442669940 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442669940 Building ZINC001442735060 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442735060 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/246 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1cccc(Cl)c1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001442735060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442735060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001442735060 none O=C(c1cccc(Cl)c1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 47, 41, 47, 47, 47, 9, 9, 9, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 9, 9, 47, 47, 47, 47, 9, 9, 9, 9, 3, 3, 3, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/247 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1cccc(Cl)c1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001442735060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442735060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001442735060 none O=C(c1cccc(Cl)c1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 22, 49, 49, 41, 49, 49, 49, 9, 10, 10, 4, 2, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 49, 49, 49, 49, 10, 10, 10, 10, 3, 1, 3, 10, 10, 10, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442735060 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060 Building ZINC001442735060 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442735060 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 246) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(c1cccc(Cl)c1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001442735060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442735060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001442735060 none O=C(c1cccc(Cl)c1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 47, 41, 47, 47, 47, 9, 9, 9, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 9, 9, 47, 47, 47, 47, 9, 9, 9, 9, 3, 3, 3, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 247) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(c1cccc(Cl)c1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001442735060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442735060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001442735060 none O=C(c1cccc(Cl)c1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 16, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 22, 49, 49, 41, 49, 49, 49, 9, 10, 10, 4, 2, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 10, 10, 49, 49, 49, 49, 10, 10, 10, 10, 3, 1, 3, 10, 10, 10, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442735060 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442735060 Building ZINC001442779647 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442779647 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/248 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCSCC2)ccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001442779647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442779647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001442779647 none Cc1cc(C(=O)N2CCSCC2)ccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 14, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 3, 6, 22, 22, 27, 27, 27, 27, 27, 9, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 3, 7, 7, 7, 7] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/249 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCSCC2)ccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001442779647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442779647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001442779647 none Cc1cc(C(=O)N2CCSCC2)ccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 14, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 3, 10, 27, 27, 32, 32, 32, 32, 31, 9, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 32, 31, 32, 31, 32, 32, 32, 31, 9, 9, 3, 7, 7, 7, 7] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442779647 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647 Building ZINC001442779647 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442779647 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 248) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cc(C(=O)N2CCSCC2)ccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001442779647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442779647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001442779647 none Cc1cc(C(=O)N2CCSCC2)ccc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 14, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 3, 6, 22, 22, 27, 27, 27, 27, 27, 9, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 3, 7, 7, 7, 7] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 249) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cc(C(=O)N2CCSCC2)ccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001442779647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442779647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001442779647 none Cc1cc(C(=O)N2CCSCC2)ccc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 14, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 3, 10, 27, 27, 32, 32, 32, 32, 31, 9, 9, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 32, 31, 32, 31, 32, 32, 32, 31, 9, 9, 3, 7, 7, 7, 7] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442779647 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442779647 Building ZINC001442808947 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442808947 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/250 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)co2)cc1) `ZINC001442808947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442808947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001442808947 none COc1ccc(c2nc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)co2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', '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, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 30, 30, 30, 15, 10, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 39, 39, 39, 39, 39, 39, 39, 15, 15, 10, 10, 3, 6, 6, 30, 39, 39] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/251 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)co2)cc1) `ZINC001442808947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442808947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001442808947 none COc1ccc(c2nc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)co2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', '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, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 30, 30, 30, 15, 10, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 39, 39, 39, 39, 39, 39, 39, 15, 15, 10, 10, 3, 6, 6, 30, 39, 39] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442808947 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947 Building ZINC001442808947 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442808947 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 250) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc(c2nc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)co2)cc1) `ZINC001442808947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442808947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001442808947 none COc1ccc(c2nc(CCNC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)co2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', '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, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 30, 30, 30, 15, 10, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 39, 39, 39, 39, 39, 39, 39, 15, 15, 10, 10, 3, 6, 6, 30, 39, 39] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 251) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc(c2nc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)co2)cc1) `ZINC001442808947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442808947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001442808947 none COc1ccc(c2nc(CCNC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)co2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', '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, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 30, 30, 30, 15, 10, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 39, 39, 39, 39, 39, 39, 39, 15, 15, 10, 10, 3, 6, 6, 30, 39, 39] 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442808947 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442808947 Building ZINC001442814823 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442814823 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/252 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nc(CCNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)co2)cc1) `ZINC001442814823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442814823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001442814823 none COc1ccc(c2nc(CCNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)co2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 26, 26, 26, 16, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 26, 26, 40, 40, 40, 40, 40, 40, 40, 16, 16, 10, 10, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 26, 40, 40] 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, 56]) total number of confs: 120 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/253 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nc(CCNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)co2)cc1) `ZINC001442814823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442814823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001442814823 none COc1ccc(c2nc(CCNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)co2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 25, 25, 25, 15, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 25, 25, 39, 39, 39, 39, 39, 39, 39, 15, 15, 10, 10, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 25, 39, 39] 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, 56]) total number of confs: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442814823 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823 Building ZINC001442814823 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001442814823 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 252) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc(c2nc(CCNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)co2)cc1) `ZINC001442814823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001442814823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001442814823 none COc1ccc(c2nc(CCNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)co2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 26, 26, 26, 16, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 26, 26, 40, 40, 40, 40, 40, 40, 40, 16, 16, 10, 10, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 26, 40, 40] 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, 56]) total number of confs: 120 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 253) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc(c2nc(CCNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)co2)cc1) `ZINC001442814823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001442814823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001442814823 none COc1ccc(c2nc(CCNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)co2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 25, 25, 25, 15, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 25, 25, 39, 39, 39, 39, 39, 39, 39, 15, 15, 10, 10, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 25, 39, 39] 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, 56]) total number of confs: 116 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001442814823 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001442814823 Building ZINC001443221452 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443221452 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/254 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@H]2CSCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1C) `ZINC001443221452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443221452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001443221452 none Cc1ccc(NC(=O)[C@@H]2CSCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 12, 37, 37, 12, 12, 5, 12, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 12, 5, 5, 5, 5, 5, 5, 5, 5, 37, 37, 37, 37] 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/255 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@H]2CSCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1C) `ZINC001443221452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443221452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001443221452 none Cc1ccc(NC(=O)[C@@H]2CSCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 8, 8, 4, 8, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 8, 4, 4, 4, 4, 5, 5, 5, 5, 33, 33, 33, 33] 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: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001443221452 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452 Building ZINC001443221452 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443221452 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 254) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(NC(=O)[C@@H]2CSCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1C) `ZINC001443221452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443221452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001443221452 none Cc1ccc(NC(=O)[C@@H]2CSCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 12, 37, 37, 12, 12, 5, 12, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 12, 5, 5, 5, 5, 5, 5, 5, 5, 37, 37, 37, 37] 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: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 255) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(NC(=O)[C@@H]2CSCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1C) `ZINC001443221452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443221452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001443221452 none Cc1ccc(NC(=O)[C@@H]2CSCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 8, 8, 4, 8, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 8, 4, 4, 4, 4, 5, 5, 5, 5, 33, 33, 33, 33] 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: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001443221452 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221452 Building ZINC001443221456 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443221456 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/256 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@H]2CSCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1C) `ZINC001443221456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443221456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001443221456 none Cc1ccc(NC(=O)[C@H]2CSCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 34, 34, 8, 8, 4, 8, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 8, 4, 4, 4, 4, 3, 3, 3, 3, 34, 34, 34, 34] 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: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/257 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@H]2CSCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1C) `ZINC001443221456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443221456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001443221456 none Cc1ccc(NC(=O)[C@H]2CSCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 14, 14, 6, 14, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 14, 6, 6, 6, 6, 4, 4, 4, 4, 40, 40, 40, 40] 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: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001443221456 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456 Building ZINC001443221456 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443221456 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 256) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(NC(=O)[C@H]2CSCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1C) `ZINC001443221456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443221456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001443221456 none Cc1ccc(NC(=O)[C@H]2CSCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 34, 34, 8, 8, 4, 8, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 34, 34, 34, 34, 34, 34, 34, 34, 8, 4, 4, 4, 4, 3, 3, 3, 3, 34, 34, 34, 34] 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: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 257) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(NC(=O)[C@H]2CSCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1C) `ZINC001443221456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443221456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001443221456 none Cc1ccc(NC(=O)[C@H]2CSCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 40, 14, 14, 6, 14, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 14, 6, 6, 6, 6, 4, 4, 4, 4, 40, 40, 40, 40] 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: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001443221456 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443221456 Building ZINC001443264521 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443264521 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/258 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCc2nc(c3ccccc3)ncc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001443264521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443264521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001443264521 none O=C(N[C@H]1CCc2nc(c3ccccc3)ncc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 23, 23, 23, 23, 23, 23, 23, 38, 38, 38, 38, 38, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 9, 4, 23, 23, 23, 23, 38, 38, 38, 38, 38, 23, 23, 23, 9, 9] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/259 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCc2nc(c3ccccc3)ncc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001443264521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443264521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001443264521 none O=C(N[C@H]1CCc2nc(c3ccccc3)ncc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 20, 20, 20, 20, 20, 20, 20, 38, 38, 38, 38, 38, 20, 20, 20, 20, 1, 1, 1, 9, 9, 9, 9, 9, 4, 20, 20, 20, 20, 38, 38, 38, 38, 38, 20, 20, 20, 9, 9] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001443264521 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521 Building ZINC001443264521 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443264521 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 258) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@H]1CCc2nc(c3ccccc3)ncc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001443264521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443264521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001443264521 none O=C(N[C@H]1CCc2nc(c3ccccc3)ncc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 23, 23, 23, 23, 23, 23, 23, 38, 38, 38, 38, 38, 23, 23, 23, 23, 1, 1, 1, 9, 9, 9, 9, 9, 4, 23, 23, 23, 23, 38, 38, 38, 38, 38, 23, 23, 23, 9, 9] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 259) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@H]1CCc2nc(c3ccccc3)ncc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001443264521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443264521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001443264521 none O=C(N[C@H]1CCc2nc(c3ccccc3)ncc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 20, 20, 20, 20, 20, 20, 20, 38, 38, 38, 38, 38, 20, 20, 20, 20, 1, 1, 1, 9, 9, 9, 9, 9, 4, 20, 20, 20, 20, 38, 38, 38, 38, 38, 20, 20, 20, 9, 9] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001443264521 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264521 Building ZINC001443264534 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443264534 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/260 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCc2nc(c3ccccc3)ncc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001443264534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443264534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001443264534 none O=C(N[C@@H]1CCc2nc(c3ccccc3)ncc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 19, 19, 19, 19, 19, 37, 37, 37, 37, 37, 19, 19, 19, 19, 1, 1, 1, 9, 9, 9, 9, 9, 4, 19, 19, 19, 19, 37, 37, 37, 37, 37, 19, 19, 19, 9, 9] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/261 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCc2nc(c3ccccc3)ncc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001443264534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443264534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001443264534 none O=C(N[C@@H]1CCc2nc(c3ccccc3)ncc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 22, 22, 22, 22, 22, 22, 22, 37, 37, 37, 37, 37, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 4, 22, 22, 22, 22, 37, 37, 37, 37, 37, 22, 22, 22, 9, 9] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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/6899/xaj-8058088.10/working/building/ZINC001443264534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001443264534 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534 Building ZINC001443264534 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443264534 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 260) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCc2nc(c3ccccc3)ncc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001443264534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443264534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001443264534 none O=C(N[C@@H]1CCc2nc(c3ccccc3)ncc2C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 19, 19, 19, 19, 19, 37, 37, 37, 37, 37, 19, 19, 19, 19, 1, 1, 1, 9, 9, 9, 9, 9, 4, 19, 19, 19, 19, 37, 37, 37, 37, 37, 19, 19, 19, 9, 9] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 261) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCc2nc(c3ccccc3)ncc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001443264534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443264534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001443264534 none O=C(N[C@@H]1CCc2nc(c3ccccc3)ncc2C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 22, 22, 22, 22, 22, 22, 22, 37, 37, 37, 37, 37, 22, 22, 22, 22, 1, 1, 1, 9, 9, 9, 9, 9, 4, 22, 22, 22, 22, 37, 37, 37, 37, 37, 22, 22, 22, 9, 9] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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/6899/xaj-8058088.10/working/building/ZINC001443264534 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001443264534 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443264534 Building ZINC001443637481 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001443637481 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/262 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC[N@]1CC[N@](c2cccc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001443637481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443637481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001443637481 none O=C(NCCC[N@]1CC[N@](c2cccc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/263 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC[N@]1CC[N@@](c2cccc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001443637481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443637481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001443637481 none O=C(NCCC[N@]1CC[N@@](c2cccc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/264 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/264' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC[N@]1CC[N@](c2cccc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001443637481.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001443637481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001443637481 none O=C(NCCC[N@]1CC[N@](c2cccc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/265 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/265' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCC[N@]1CC[N@@](c2cccc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001443637481.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001443637481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001443637481 none O=C(NCCC[N@]1CC[N@@](c2cccc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001443637481 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 Building ZINC001443637481 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001443637481 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 262) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCCC[N@]1CC[N@](c2cccc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001443637481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443637481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001443637481 none O=C(NCCC[N@]1CC[N@](c2cccc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 263) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCCC[N@]1CC[N@@](c2cccc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001443637481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443637481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001443637481 none O=C(NCCC[N@]1CC[N@@](c2cccc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 264) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NCCC[N@]1CC[N@](c2cccc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001443637481.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001443637481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001443637481 none O=C(NCCC[N@]1CC[N@](c2cccc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 265) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NCCC[N@]1CC[N@@](c2cccc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001443637481.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001443637481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001443637481 none O=C(NCCC[N@]1CC[N@@](c2cccc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001443637481 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 Building ZINC001443637481 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001443637481 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 262) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCCC[N@]1CC[N@](c2cccc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001443637481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443637481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001443637481 none O=C(NCCC[N@]1CC[N@](c2cccc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 263) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCCC[N@]1CC[N@@](c2cccc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001443637481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443637481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001443637481 none O=C(NCCC[N@]1CC[N@@](c2cccc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 264) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NCCC[N@]1CC[N@](c2cccc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001443637481.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001443637481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001443637481 none O=C(NCCC[N@]1CC[N@](c2cccc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 265) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NCCC[N@]1CC[N@@](c2cccc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001443637481.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001443637481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001443637481 none O=C(NCCC[N@]1CC[N@@](c2cccc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001443637481 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 Building ZINC001443637481 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001443637481 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 262) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCCC[N@]1CC[N@](c2cccc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001443637481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443637481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001443637481 none O=C(NCCC[N@]1CC[N@](c2cccc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 263) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCCC[N@]1CC[N@@](c2cccc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001443637481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443637481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001443637481 none O=C(NCCC[N@]1CC[N@@](c2cccc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 18, 18, 18, 18, 50, 50, 50, 50, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 264) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NCCC[N@]1CC[N@](c2cccc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001443637481.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001443637481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001443637481 none O=C(NCCC[N@]1CC[N@](c2cccc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 265) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NCCC[N@]1CC[N@@](c2cccc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001443637481.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001443637481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001443637481 none O=C(NCCC[N@]1CC[N@@](c2cccc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 17, 17, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 11, 11, 11, 11, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001443637481 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443637481 Building ZINC001443641777 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443641777 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/266 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)Nc1ccc(C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001443641777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443641777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001443641777 none CS(=O)(=O)Nc1ccc(C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [28, 19, 28, 28, 10, 10, 10, 7, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 28, 28, 28, 19, 10, 10, 10, 3, 7, 7, 7, 7] 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: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/267 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)Nc1ccc(C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001443641777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443641777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001443641777 none CS(=O)(=O)Nc1ccc(C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [30, 21, 30, 30, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 21, 11, 11, 11, 4, 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001443641777 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777 Building ZINC001443641777 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443641777 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 266) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CS(=O)(=O)Nc1ccc(C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001443641777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443641777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001443641777 none CS(=O)(=O)Nc1ccc(C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [28, 19, 28, 28, 10, 10, 10, 7, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 28, 28, 28, 19, 10, 10, 10, 3, 7, 7, 7, 7] 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: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 267) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CS(=O)(=O)Nc1ccc(C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001443641777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443641777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001443641777 none CS(=O)(=O)Nc1ccc(C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 14, 11, 11, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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: [30, 21, 30, 30, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 21, 11, 11, 11, 4, 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: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001443641777 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443641777 Building ZINC001443683381 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443683381 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/268 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001443683381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443683381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001443683381 none O=C(Nc1ccc(Cl)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 16, 26, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 7, 1, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 33, 33, 33, 33, 33, 16, 16, 16, 16, 4, 4, 4, 4, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/269 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Cl)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001443683381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443683381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001443683381 none O=C(Nc1ccc(Cl)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 24, 31, 31, 31, 31, 31, 31, 31, 18, 18, 18, 7, 1, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 31, 31, 31, 31, 31, 18, 18, 18, 18, 4, 4, 4, 4, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 88 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001443683381 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381 Building ZINC001443683381 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001443683381 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 268) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(Cl)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001443683381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001443683381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001443683381 none O=C(Nc1ccc(Cl)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 16, 26, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 7, 1, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 33, 33, 33, 33, 33, 16, 16, 16, 16, 4, 4, 4, 4, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 98 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 269) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(Cl)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001443683381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001443683381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001443683381 none O=C(Nc1ccc(Cl)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 24, 31, 31, 31, 31, 31, 31, 31, 18, 18, 18, 7, 1, 9, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 31, 31, 31, 31, 31, 18, 18, 18, 18, 4, 4, 4, 4, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 88 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001443683381 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001443683381 Building ZINC001444049660 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001444049660 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/270 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1) `ZINC001444049660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001444049660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001444049660 none CN(C(=O)[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 14, 8, 14, 3, 8, 8, 14, 14, 14, 14, 14, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 32, 32, 32, 32, 32, 31, 31, 31, 14, 14, 14, 14, 14, 14, 14, 3, 4, 4, 4, 4, 32, 32, 32, 32, 32] 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, 53, 54]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/271 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1) `ZINC001444049660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001444049660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001444049660 none CN(C(=O)[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 6, 12, 3, 6, 6, 12, 12, 12, 12, 12, 12, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 29, 29, 29, 29, 29, 26, 26, 26, 12, 12, 12, 12, 12, 12, 12, 3, 4, 4, 4, 4, 29, 29, 29, 29, 29] 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, 53, 54]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001444049660 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660 Building ZINC001444049660 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001444049660 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 270) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C(=O)[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1) `ZINC001444049660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001444049660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001444049660 none CN(C(=O)[C@H](Cc1ccccc1)NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 14, 8, 14, 3, 8, 8, 14, 14, 14, 14, 14, 14, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 32, 32, 32, 32, 32, 31, 31, 31, 14, 14, 14, 14, 14, 14, 14, 3, 4, 4, 4, 4, 32, 32, 32, 32, 32] 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, 53, 54]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 271) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C(=O)[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1) `ZINC001444049660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001444049660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001444049660 none CN(C(=O)[C@H](Cc1ccccc1)NC(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 6, 12, 3, 6, 6, 12, 12, 12, 12, 12, 12, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 29, 29, 29, 29, 29, 26, 26, 26, 12, 12, 12, 12, 12, 12, 12, 3, 4, 4, 4, 4, 29, 29, 29, 29, 29] 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, 53, 54]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001444049660 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444049660 Building ZINC001444932878 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001444932878 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/272 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(Cc2ccsc2)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1OC) `ZINC001444932878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001444932878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001444932878 none COc1ccc(CCN(Cc2ccsc2)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 14, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [23, 12, 12, 12, 12, 7, 7, 5, 3, 5, 6, 12, 12, 12, 12, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 12, 23, 23, 23, 23, 12, 12, 7, 7, 7, 7, 6, 6, 12, 12, 12, 2, 2, 4, 2, 2, 12, 23, 23, 23] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/273 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCN(Cc2ccsc2)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1OC) `ZINC001444932878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001444932878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001444932878 none COc1ccc(CCN(Cc2ccsc2)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 14, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [23, 12, 12, 12, 12, 7, 7, 5, 3, 5, 6, 12, 12, 12, 12, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 12, 23, 23, 23, 23, 12, 12, 7, 7, 7, 7, 6, 6, 12, 12, 12, 2, 2, 4, 2, 2, 12, 23, 23, 23] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001444932878 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878 Building ZINC001444932878 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001444932878 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 272) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc(CCN(Cc2ccsc2)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1OC) `ZINC001444932878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001444932878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001444932878 none COc1ccc(CCN(Cc2ccsc2)C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 14, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [23, 12, 12, 12, 12, 7, 7, 5, 3, 5, 6, 12, 12, 12, 12, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 12, 23, 23, 23, 23, 12, 12, 7, 7, 7, 7, 6, 6, 12, 12, 12, 2, 2, 4, 2, 2, 12, 23, 23, 23] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 273) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc(CCN(Cc2ccsc2)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1OC) `ZINC001444932878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001444932878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001444932878 none COc1ccc(CCN(Cc2ccsc2)C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 14, 1, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [23, 12, 12, 12, 12, 7, 7, 5, 3, 5, 6, 12, 12, 12, 12, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 12, 23, 23, 23, 23, 12, 12, 7, 7, 7, 7, 6, 6, 12, 12, 12, 2, 2, 4, 2, 2, 12, 23, 23, 23] 100 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001444932878 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001444932878 Building ZINC001445367889 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001445367889 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/274 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(Oc2ccccc2I)CC1) `ZINC001445367889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445367889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001445367889 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(Oc2ccccc2I)CC1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 18, 5, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 2, 2, 3, 3, 3, 3, 12, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 40 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/275 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(Oc2ccccc2I)CC1) `ZINC001445367889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445367889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001445367889 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(Oc2ccccc2I)CC1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 18, 5, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 2, 2, 4, 4, 4, 4, 13, 18, 18, 15, 18, 18, 18, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 18, 18, 18, 18, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001445367889 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889 Building ZINC001445367889 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001445367889 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 274) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(Oc2ccccc2I)CC1) `ZINC001445367889.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445367889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001445367889 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(Oc2ccccc2I)CC1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 18, 5, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 2, 2, 3, 3, 3, 3, 12, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 40 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 275) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(Oc2ccccc2I)CC1) `ZINC001445367889.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445367889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001445367889 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(Oc2ccccc2I)CC1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 18, 5, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 2, 2, 4, 4, 4, 4, 13, 18, 18, 15, 18, 18, 18, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 18, 18, 18, 18, 4, 4, 4, 4] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001445367889 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445367889 Building ZINC001445491456 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001445491456 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/276 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1ccccc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001445491456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445491456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001445491456 none COCCOc1ccccc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 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] dock color type numbers: [7, 3, 7, 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: [50, 50, 50, 42, 22, 22, 22, 7, 22, 22, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/277 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1ccccc1N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001445491456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445491456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001445491456 none COCCOc1ccccc1N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 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] dock color type numbers: [7, 3, 7, 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: [50, 50, 50, 43, 22, 22, 22, 7, 22, 22, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001445491456 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456 Building ZINC001445491456 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001445491456 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 276) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COCCOc1ccccc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001445491456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445491456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001445491456 none COCCOc1ccccc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 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] dock color type numbers: [7, 3, 7, 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: [50, 50, 50, 42, 22, 22, 22, 7, 22, 22, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 277) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COCCOc1ccccc1N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001445491456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445491456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001445491456 none COCCOc1ccccc1N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 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] dock color type numbers: [7, 3, 7, 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: [50, 50, 50, 43, 22, 22, 22, 7, 22, 22, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001445491456 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445491456 Building ZINC001445703843 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001445703843 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/278 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445703843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703843 none O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 13, 13, 27, 27, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/279 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445703843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703843 none O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 15, 15, 32, 32, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/280 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/280' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703843.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001445703843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703843 none O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 13, 13, 27, 27, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/281 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/281' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703843.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001445703843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703843 none O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 15, 15, 32, 32, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001445703843 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 Building ZINC001445703843 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001445703843 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 278) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445703843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703843 none O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 13, 13, 27, 27, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 279) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445703843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703843 none O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 15, 15, 32, 32, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 280) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703843.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001445703843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703843 none O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 13, 13, 27, 27, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 281) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703843.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001445703843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703843 none O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 15, 15, 32, 32, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001445703843 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 Building ZINC001445703843 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001445703843 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 278) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445703843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703843 none O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 13, 13, 27, 27, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 279) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445703843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703843 none O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 15, 15, 32, 32, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 280) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703843.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001445703843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703843 none O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 13, 13, 27, 27, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 281) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703843.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001445703843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703843 none O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 15, 15, 32, 32, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001445703843 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 Building ZINC001445703843 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001445703843 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 278) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445703843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703843 none O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 13, 13, 27, 27, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 279) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445703843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703843 none O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 15, 15, 32, 32, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 280) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703843.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001445703843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703843 none O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 4, 13, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 13, 13, 13, 13, 27, 27, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 281) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703843.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001445703843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703843 none O=C(N[C@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 15, 15, 32, 32, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001445703843 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703843 Building ZINC001445703852 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001445703852 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/282 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445703852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703852 none O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 15, 15, 30, 30, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/283 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445703852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703852 none O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 4, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 14, 14, 14, 14, 28, 28, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/284 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/284' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703852.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001445703852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703852 none O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 15, 15, 30, 30, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/285 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/285' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703852.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001445703852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703852 none O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 4, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 14, 14, 14, 14, 28, 28, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001445703852 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 Building ZINC001445703852 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001445703852 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 282) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445703852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703852 none O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 15, 15, 30, 30, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 283) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445703852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703852 none O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 4, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 14, 14, 14, 14, 28, 28, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 284) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703852.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001445703852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703852 none O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 15, 15, 30, 30, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 285) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703852.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001445703852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703852 none O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 4, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 14, 14, 14, 14, 28, 28, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001445703852 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 Building ZINC001445703852 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001445703852 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 282) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445703852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703852 none O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 15, 15, 30, 30, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 283) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445703852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703852 none O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 4, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 14, 14, 14, 14, 28, 28, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 284) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703852.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001445703852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703852 none O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 15, 15, 30, 30, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 285) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703852.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001445703852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703852 none O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 4, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 14, 14, 14, 14, 28, 28, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001445703852 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 Building ZINC001445703852 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001445703852 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 282) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445703852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703852 none O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 15, 15, 30, 30, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 283) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445703852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703852 none O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 4, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 14, 14, 14, 14, 28, 28, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 284) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703852.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001445703852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703852 none O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 5, 15, 15, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 15, 15, 30, 30, 15, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 285) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001445703852.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001445703852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001445703852 none O=C(N[C@@H]1CCN(c2ncc(C(F)(F)F)cc2Cl)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', '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, 5, 7, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 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, 3, 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] 0 hydrogens need 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, 4, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 14, 14, 14, 14, 28, 28, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001445703852 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001445703852 Building ZINC001446156629 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446156629 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/286 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)cc(OCC(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001446156629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446156629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001446156629 none Cc1cc(C)cc(OCC(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 50, 50, 49, 20, 10, 9, 10, 9, 9, 9, 5, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 49, 50, 50, 50, 50, 20, 20, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9, 50] 50 rigid atoms, others: [44, 45, 46, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50, 51]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/287 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)cc(OCC(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001446156629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446156629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001446156629 none Cc1cc(C)cc(OCC(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 14, 10, 14, 10, 10, 10, 5, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 10, 10, 10, 10, 1, 1, 1, 10, 10, 10, 10, 50] 50 rigid atoms, others: [44, 45, 46, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50, 51]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001446156629 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629 Building ZINC001446156629 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446156629 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 286) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cc(C)cc(OCC(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001446156629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446156629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001446156629 none Cc1cc(C)cc(OCC(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 50, 50, 49, 20, 10, 9, 10, 9, 9, 9, 5, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 49, 50, 50, 50, 50, 20, 20, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9, 50] 50 rigid atoms, others: [44, 45, 46, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50, 51]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 287) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cc(C)cc(OCC(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1) `ZINC001446156629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446156629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001446156629 none Cc1cc(C)cc(OCC(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 22, 14, 10, 14, 10, 10, 10, 5, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 10, 10, 10, 10, 1, 1, 1, 10, 10, 10, 10, 50] 50 rigid atoms, others: [44, 45, 46, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50, 51]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001446156629 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446156629 Building ZINC001446243118 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446243118 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/288 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1)C(=O)OC(C)(C)C) `ZINC001446243118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446243118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001446243118 none CN(CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 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: [27, 10, 9, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 27, 38, 38, 38, 38, 38, 38, 27, 27, 27, 10, 10, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38] 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, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/289 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCC1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1)C(=O)OC(C)(C)C) `ZINC001446243118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446243118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001446243118 none CN(CCC1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 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: [30, 13, 11, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 30, 40, 40, 42, 42, 42, 42, 30, 30, 30, 13, 13, 11, 11, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4, 42, 42, 42, 42, 42, 42, 42, 42, 42] 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, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001446243118 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118 Building ZINC001446243118 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446243118 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 288) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1)C(=O)OC(C)(C)C) `ZINC001446243118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446243118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001446243118 none CN(CCC1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 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: [27, 10, 9, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 27, 38, 38, 38, 38, 38, 38, 27, 27, 27, 10, 10, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 38, 38, 38, 38, 38, 38, 38, 38, 38] 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, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 289) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(CCC1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1)C(=O)OC(C)(C)C) `ZINC001446243118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446243118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001446243118 none CN(CCC1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 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: [30, 13, 11, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 30, 40, 40, 42, 42, 42, 42, 30, 30, 30, 13, 13, 11, 11, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4, 42, 42, 42, 42, 42, 42, 42, 42, 42] 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, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001446243118 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446243118 Building ZINC001446989010 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446989010 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/290 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/290' -> `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)N1C[C@H](C)N(C(=O)OC(C)(C)C)C[C@H]1C) `ZINC001446989010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446989010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001446989010 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)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', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 8, 8, 3, 3, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 19, 19, 30, 30, 30, 30, 5, 5, 5, 5, 3, 3, 3, 8, 8, 8, 8, 8, 3, 3, 3, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 88 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/291 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/291' -> `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)N1C[C@H](C)N(C(=O)OC(C)(C)C)C[C@H]1C) `ZINC001446989010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446989010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001446989010 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)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', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 20, 20, 30, 30, 30, 30, 7, 7, 7, 7, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 4, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 30, 7, 7, 7, 7, 7] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 102 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001446989010 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010 Building ZINC001446989010 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446989010 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 290) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)C[C@H]1C) `ZINC001446989010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446989010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001446989010 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)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', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 8, 8, 3, 3, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 5, 5, 19, 19, 30, 30, 30, 30, 5, 5, 5, 5, 3, 3, 3, 8, 8, 8, 8, 8, 3, 3, 3, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 88 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 291) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)C[C@H]1C) `ZINC001446989010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446989010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001446989010 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)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', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 20, 20, 30, 30, 30, 30, 7, 7, 7, 7, 4, 4, 4, 14, 14, 4, 14, 14, 4, 4, 4, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 30, 7, 7, 7, 7, 7] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 102 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001446989010 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989010 Building ZINC001446989033 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446989033 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/292 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/292' -> `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)N1C[C@H](C)N(C(=O)OC(C)(C)C)C[C@@H]1C) `ZINC001446989033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446989033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001446989033 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)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', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 8, 8, 3, 3, 1, 1, 1, 2, 7, 7, 8, 8, 8, 8, 8, 8, 22, 22, 34, 35, 35, 35, 8, 8, 8, 8, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 8, 8, 8, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 103 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/293 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/293' -> `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)N1C[C@H](C)N(C(=O)OC(C)(C)C)C[C@@H]1C) `ZINC001446989033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446989033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001446989033 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)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', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21, 33, 33, 33, 33, 7, 7, 7, 7, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 7, 7, 7, 7, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 94 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001446989033 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033 Building ZINC001446989033 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446989033 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 292) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)C[C@@H]1C) `ZINC001446989033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446989033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001446989033 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)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', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 8, 8, 3, 3, 1, 1, 1, 2, 7, 7, 8, 8, 8, 8, 8, 8, 22, 22, 34, 35, 35, 35, 8, 8, 8, 8, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 8, 8, 8, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 8, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 103 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 293) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)C[C@@H]1C) `ZINC001446989033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446989033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001446989033 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)N(C(=O)OC(C)(C)C)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', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 7, 7, 7, 7, 7, 7, 7, 7, 21, 21, 33, 33, 33, 33, 7, 7, 7, 7, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 7, 7, 7, 7, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 94 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001446989033 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989033 Building ZINC001446989035 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446989035 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/294 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/294' -> `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)N1C[C@@H](C)N(C(=O)OC(C)(C)C)C[C@H]1C) `ZINC001446989035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446989035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001446989035 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)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', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 9, 9, 3, 3, 1, 1, 1, 2, 5, 5, 6, 6, 6, 6, 6, 6, 16, 16, 26, 26, 26, 26, 6, 6, 6, 6, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 83 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/295 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/295' -> `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)N1C[C@@H](C)N(C(=O)OC(C)(C)C)C[C@H]1C) `ZINC001446989035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446989035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001446989035 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)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', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need 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, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 2, 6, 6, 7, 7, 7, 7, 7, 7, 17, 17, 30, 30, 30, 30, 7, 7, 7, 7, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 30, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 86 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001446989035 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035 Building ZINC001446989035 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446989035 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 294) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)C[C@H]1C) `ZINC001446989035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446989035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001446989035 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)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', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 9, 9, 3, 3, 1, 1, 1, 2, 5, 5, 6, 6, 6, 6, 6, 6, 16, 16, 26, 26, 26, 26, 6, 6, 6, 6, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 83 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 295) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)C[C@H]1C) `ZINC001446989035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446989035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001446989035 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)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', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need 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, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 2, 6, 6, 7, 7, 7, 7, 7, 7, 17, 17, 30, 30, 30, 30, 7, 7, 7, 7, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 30, 7, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 86 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001446989035 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989035 Building ZINC001446989038 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446989038 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/296 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/296' -> `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)N1C[C@@H](C)N(C(=O)OC(C)(C)C)C[C@@H]1C) `ZINC001446989038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446989038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001446989038 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)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', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need 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, 10, 10, 7, 10, 10, 4, 4, 1, 1, 1, 1, 5, 6, 8, 8, 8, 8, 8, 8, 24, 24, 38, 40, 40, 40, 8, 8, 8, 8, 4, 4, 4, 10, 10, 6, 10, 10, 4, 4, 4, 8, 8, 8, 8, 8, 40, 40, 40, 40, 40, 40, 40, 40, 40, 8, 8, 8, 8, 8] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 120 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/297 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/297' -> `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)N1C[C@@H](C)N(C(=O)OC(C)(C)C)C[C@@H]1C) `ZINC001446989038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446989038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001446989038 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)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', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 10, 10, 3, 3, 1, 1, 1, 1, 4, 5, 7, 7, 7, 7, 7, 7, 17, 17, 31, 32, 32, 32, 7, 7, 7, 7, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 3, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 96 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001446989038 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038 Building ZINC001446989038 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001446989038 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 296) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)C[C@@H]1C) `ZINC001446989038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001446989038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001446989038 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)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', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need 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, 10, 10, 7, 10, 10, 4, 4, 1, 1, 1, 1, 5, 6, 8, 8, 8, 8, 8, 8, 24, 24, 38, 40, 40, 40, 8, 8, 8, 8, 4, 4, 4, 10, 10, 6, 10, 10, 4, 4, 4, 8, 8, 8, 8, 8, 40, 40, 40, 40, 40, 40, 40, 40, 40, 8, 8, 8, 8, 8] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 120 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 297) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)C[C@@H]1C) `ZINC001446989038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001446989038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001446989038 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)N(C(=O)OC(C)(C)C)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', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 10, 10, 3, 3, 1, 1, 1, 1, 4, 5, 7, 7, 7, 7, 7, 7, 17, 17, 31, 32, 32, 32, 7, 7, 7, 7, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 3, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 96 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001446989038 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001446989038 Building ZINC001448231814 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448231814 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/298 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001448231814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448231814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001448231814 none COc1ccccc1[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 14, 14, 14, 12, 14, 14, 9, 9, 9, 9, 9, 9, 19, 19, 38, 39, 39, 39, 9, 9, 9, 2, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 14, 14, 14, 14, 9, 9, 39, 39, 39, 39, 39, 39, 39, 39, 39, 9, 9, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/299 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001448231814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448231814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001448231814 none COc1ccccc1[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens 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, 9, 16, 16, 8, 8, 8, 8, 8, 8, 19, 19, 37, 37, 37, 37, 8, 8, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 16, 16, 16, 16, 8, 8, 37, 37, 37, 37, 37, 37, 37, 37, 37, 8, 8, 8, 8, 1, 1, 1, 1] 50 rigid atoms, others: [32, 56, 58, 57, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001448231814 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814 Building ZINC001448231814 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448231814 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 298) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001448231814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448231814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001448231814 none COc1ccccc1[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 14, 14, 14, 12, 14, 14, 9, 9, 9, 9, 9, 9, 19, 19, 38, 39, 39, 39, 9, 9, 9, 2, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 14, 14, 14, 14, 9, 9, 39, 39, 39, 39, 39, 39, 39, 39, 39, 9, 9, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 299) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001448231814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448231814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001448231814 none COc1ccccc1[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens 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, 9, 16, 16, 8, 8, 8, 8, 8, 8, 19, 19, 37, 37, 37, 37, 8, 8, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 16, 16, 16, 16, 8, 8, 37, 37, 37, 37, 37, 37, 37, 37, 37, 8, 8, 8, 8, 1, 1, 1, 1] 50 rigid atoms, others: [32, 56, 58, 57, 55, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001448231814 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231814 Building ZINC001448231816 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448231816 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/300 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001448231816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448231816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001448231816 none COc1ccccc1[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 12, 15, 15, 9, 9, 9, 9, 9, 9, 19, 19, 36, 38, 38, 38, 9, 9, 7, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 18, 15, 15, 15, 15, 9, 9, 38, 38, 38, 38, 38, 38, 38, 38, 38, 9, 9, 9, 9, 2, 2, 2, 2] 50 rigid atoms, others: [22, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/301 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001448231816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448231816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001448231816 none COc1ccccc1[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 14, 14, 12, 14, 14, 9, 9, 9, 9, 9, 9, 19, 19, 38, 40, 40, 40, 9, 9, 9, 2, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 16, 16, 16, 14, 14, 14, 14, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 9, 9, 9, 9, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001448231816 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816 Building ZINC001448231816 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001448231816 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 300) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001448231816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001448231816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001448231816 none COc1ccccc1[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(F)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens 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, 15, 15, 15, 12, 15, 15, 9, 9, 9, 9, 9, 9, 19, 19, 36, 38, 38, 38, 9, 9, 7, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 18, 18, 18, 15, 15, 15, 15, 9, 9, 38, 38, 38, 38, 38, 38, 38, 38, 38, 9, 9, 9, 9, 2, 2, 2, 2] 50 rigid atoms, others: [22, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 301) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001448231816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001448231816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001448231816 none COc1ccccc1[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(F)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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 14, 14, 12, 14, 14, 9, 9, 9, 9, 9, 9, 19, 19, 38, 40, 40, 40, 9, 9, 9, 2, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 16, 16, 16, 14, 14, 14, 14, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 9, 9, 9, 9, 2, 2, 2, 2] 50 rigid atoms, others: [24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001448231816 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001448231816 Building ZINC001449047886 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449047886 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/302 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O)(c2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001449047886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449047886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001449047886 none O=C(N1CCC(O)(c2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 4, 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] 1 hydrogens 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, 10, 15, 15, 15, 15, 15, 29, 29, 29, 29, 29, 29, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 45, 29, 29, 29, 29, 15, 15, 15, 15, 5, 5] 150 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]) total number of confs: 100 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/303 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(O)(c2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001449047886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449047886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001449047886 none O=C(N1CCC(O)(c2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 4, 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] 1 hydrogens 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, 10, 15, 15, 15, 15, 15, 31, 31, 31, 31, 31, 31, 15, 15, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 15, 15, 45, 31, 31, 31, 31, 15, 15, 15, 15, 3, 3] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 103 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449047886 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886 Building ZINC001449047886 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449047886 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 302) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCC(O)(c2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001449047886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449047886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001449047886 none O=C(N1CCC(O)(c2ccccc2Cl)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 4, 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] 1 hydrogens 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, 10, 15, 15, 15, 15, 15, 29, 29, 29, 29, 29, 29, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 15, 45, 29, 29, 29, 29, 15, 15, 15, 15, 5, 5] 150 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]) total number of confs: 100 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 303) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCC(O)(c2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001449047886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449047886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001449047886 none O=C(N1CCC(O)(c2ccccc2Cl)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 4, 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] 1 hydrogens 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, 10, 15, 15, 15, 15, 15, 31, 31, 31, 31, 31, 31, 15, 15, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 15, 15, 45, 31, 31, 31, 31, 15, 15, 15, 15, 3, 3] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 103 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449047886 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449047886 Building ZINC001449576834 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449576834 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/304 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC2(C)C)CC1) `ZINC001449576834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449576834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449576834 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC2(C)C)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 9, 9, 9, 9, 14, 14, 14, 30, 30, 41, 41, 41, 41, 14, 14, 14, 14, 9, 9, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41, 14, 14, 14, 14, 14, 14, 14, 14, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 119 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/305 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC2(C)C)CC1) `ZINC001449576834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449576834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449576834 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC2(C)C)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 4, 9, 9, 9, 9, 15, 15, 15, 37, 37, 47, 47, 47, 47, 15, 15, 15, 15, 9, 9, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 15, 15, 15, 15, 15, 15, 15, 15, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 135 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449576834 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834 Building ZINC001449576834 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449576834 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 304) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC2(C)C)CC1) `ZINC001449576834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449576834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449576834 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC2(C)C)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 5, 9, 9, 9, 9, 14, 14, 14, 30, 30, 41, 41, 41, 41, 14, 14, 14, 14, 9, 9, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 41, 41, 41, 41, 41, 41, 41, 41, 41, 14, 14, 14, 14, 14, 14, 14, 14, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 119 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 305) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC2(C)C)CC1) `ZINC001449576834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449576834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449576834 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@@H]2N(C(=O)OC(C)(C)C)CC2(C)C)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 4, 9, 9, 9, 9, 15, 15, 15, 37, 37, 47, 47, 47, 47, 15, 15, 15, 15, 9, 9, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 15, 15, 15, 15, 15, 15, 15, 15, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 135 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449576834 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576834 Building ZINC001449576871 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449576871 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/306 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC2(C)C)CC1) `ZINC001449576871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449576871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449576871 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC2(C)C)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 5, 8, 8, 8, 8, 14, 14, 14, 32, 32, 43, 43, 43, 43, 14, 14, 14, 14, 8, 8, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 43, 43, 43, 43, 43, 43, 43, 43, 43, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 126 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/307 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC2(C)C)CC1) `ZINC001449576871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449576871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449576871 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC2(C)C)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 5, 8, 8, 8, 8, 15, 15, 15, 39, 39, 46, 46, 46, 46, 15, 15, 15, 15, 8, 8, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 46, 46, 46, 46, 46, 46, 46, 46, 46, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 136 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449576871 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871 Building ZINC001449576871 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449576871 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 306) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC2(C)C)CC1) `ZINC001449576871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449576871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449576871 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC2(C)C)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 5, 8, 8, 8, 8, 14, 14, 14, 32, 32, 43, 43, 43, 43, 14, 14, 14, 14, 8, 8, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 43, 43, 43, 43, 43, 43, 43, 43, 43, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 126 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 307) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC2(C)C)CC1) `ZINC001449576871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449576871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449576871 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC([C@H]2N(C(=O)OC(C)(C)C)CC2(C)C)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 5, 8, 8, 8, 8, 15, 15, 15, 39, 39, 46, 46, 46, 46, 15, 15, 15, 15, 8, 8, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 46, 46, 46, 46, 46, 46, 46, 46, 46, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 136 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449576871 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449576871 Building ZINC001449683089 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449683089 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/308 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1) `ZINC001449683089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449683089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001449683089 none CC(C)(C)OC(=O)N1CC[C@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 25, 14, 14, 14, 8, 14, 8, 9, 8, 8, 8, 6, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 8, 8, 14, 14] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 101 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/309 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1) `ZINC001449683089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449683089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001449683089 none CC(C)(C)OC(=O)N1CC[C@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 31, 31, 24, 14, 24, 14, 14, 14, 7, 14, 7, 9, 7, 7, 7, 4, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 14, 14, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7, 14, 14] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449683089 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089 Building ZINC001449683089 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449683089 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 308) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1) `ZINC001449683089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449683089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001449683089 none CC(C)(C)OC(=O)N1CC[C@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 25, 14, 14, 14, 8, 14, 8, 9, 8, 8, 8, 6, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 14, 32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 14, 14, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 8, 8, 14, 14] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 101 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 309) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1) `ZINC001449683089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449683089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001449683089 none CC(C)(C)OC(=O)N1CC[C@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 31, 31, 24, 14, 24, 14, 14, 14, 7, 14, 7, 9, 7, 7, 7, 4, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 14, 14, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 7, 7, 14, 14] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449683089 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683089 Building ZINC001449683096 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449683096 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/310 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1) `ZINC001449683096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449683096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001449683096 none CC(C)(C)OC(=O)N1CC[C@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 38, 38, 28, 17, 28, 17, 17, 17, 10, 17, 10, 10, 10, 10, 10, 4, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 17, 38, 38, 38, 38, 38, 38, 38, 38, 38, 17, 17, 17, 17, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10, 17, 17] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/311 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1) `ZINC001449683096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449683096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001449683096 none CC(C)(C)OC(=O)N1CC[C@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 30, 19, 30, 19, 19, 19, 10, 19, 10, 11, 10, 10, 10, 6, 2, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 19, 39, 39, 39, 39, 39, 39, 39, 39, 39, 19, 19, 19, 19, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 10, 10, 19, 19] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 113 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449683096 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096 Building ZINC001449683096 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449683096 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 310) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1) `ZINC001449683096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449683096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001449683096 none CC(C)(C)OC(=O)N1CC[C@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 38, 38, 28, 17, 28, 17, 17, 17, 10, 17, 10, 10, 10, 10, 10, 4, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 17, 38, 38, 38, 38, 38, 38, 38, 38, 38, 17, 17, 17, 17, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10, 17, 17] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 311) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1) `ZINC001449683096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449683096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001449683096 none CC(C)(C)OC(=O)N1CC[C@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 30, 19, 30, 19, 19, 19, 10, 19, 10, 11, 10, 10, 10, 6, 2, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 19, 39, 39, 39, 39, 39, 39, 39, 39, 39, 19, 19, 19, 19, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 10, 10, 19, 19] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 113 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449683096 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683096 Building ZINC001449683099 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449683099 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/312 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1) `ZINC001449683099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449683099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001449683099 none CC(C)(C)OC(=O)N1CC[C@@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 29, 19, 29, 19, 19, 19, 9, 19, 9, 10, 9, 9, 9, 6, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 19, 38, 38, 38, 38, 38, 38, 38, 38, 38, 19, 19, 19, 19, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 9, 9, 19, 19] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/313 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1) `ZINC001449683099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449683099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001449683099 none CC(C)(C)OC(=O)N1CC[C@@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 15, 24, 15, 15, 15, 10, 15, 10, 10, 10, 10, 10, 4, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 15, 31, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10, 15, 15] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449683099 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099 Building ZINC001449683099 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449683099 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 312) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)(C)OC(=O)N1CC[C@@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1) `ZINC001449683099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449683099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001449683099 none CC(C)(C)OC(=O)N1CC[C@@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 29, 19, 29, 19, 19, 19, 9, 19, 9, 10, 9, 9, 9, 6, 2, 8, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 19, 38, 38, 38, 38, 38, 38, 38, 38, 38, 19, 19, 19, 19, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 9, 9, 19, 19] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 313) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)(C)OC(=O)N1CC[C@@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1) `ZINC001449683099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449683099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001449683099 none CC(C)(C)OC(=O)N1CC[C@@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 15, 24, 15, 15, 15, 10, 15, 10, 10, 10, 10, 10, 4, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 15, 31, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10, 15, 15] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449683099 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683099 Building ZINC001449683102 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449683102 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/314 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1) `ZINC001449683102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449683102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001449683102 none CC(C)(C)OC(=O)N1CC[C@@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 31, 31, 24, 14, 24, 14, 14, 14, 7, 14, 7, 9, 7, 7, 7, 4, 2, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 14, 14, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 7, 7, 14, 14] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 104 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/315 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1) `ZINC001449683102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449683102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001449683102 none CC(C)(C)OC(=O)N1CC[C@@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 33, 33, 24, 15, 24, 15, 15, 15, 8, 15, 8, 9, 8, 8, 8, 6, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 15, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 8, 8, 15, 15] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 100 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449683102 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102 Building ZINC001449683102 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449683102 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 314) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)(C)OC(=O)N1CC[C@@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1) `ZINC001449683102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449683102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001449683102 none CC(C)(C)OC(=O)N1CC[C@@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 31, 31, 24, 14, 24, 14, 14, 14, 7, 14, 7, 9, 7, 7, 7, 4, 2, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 14, 14, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 7, 7, 14, 14] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 104 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 315) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)(C)OC(=O)N1CC[C@@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1) `ZINC001449683102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449683102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001449683102 none CC(C)(C)OC(=O)N1CC[C@@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 33, 33, 24, 15, 24, 15, 15, 15, 8, 15, 8, 9, 8, 8, 8, 6, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 15, 15, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 8, 8, 15, 15] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 100 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449683102 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449683102 Building ZINC001449704757 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449704757 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/316 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001449704757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449704757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449704757 none CC(C)(C)OC(=O)N1CC[C@@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 22, 12, 22, 12, 12, 12, 9, 12, 9, 10, 9, 9, 9, 3, 2, 7, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 9, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 9, 9, 9, 9, 9, 9, 3, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 12, 12] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/317 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001449704757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449704757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449704757 none CC(C)(C)OC(=O)N1CC[C@@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 30, 30, 21, 13, 21, 13, 13, 13, 5, 13, 5, 6, 5, 5, 5, 4, 2, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449704757 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757 Building ZINC001449704757 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449704757 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 316) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001449704757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449704757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449704757 none CC(C)(C)OC(=O)N1CC[C@@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 22, 12, 22, 12, 12, 12, 9, 12, 9, 10, 9, 9, 9, 3, 2, 7, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 9, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 9, 9, 9, 9, 9, 9, 3, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 12, 12] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 317) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001449704757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449704757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449704757 none CC(C)(C)OC(=O)N1CC[C@@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 30, 30, 21, 13, 21, 13, 13, 13, 5, 13, 5, 6, 5, 5, 5, 4, 2, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 13, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449704757 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704757 Building ZINC001449704760 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449704760 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/318 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001449704760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449704760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449704760 none CC(C)(C)OC(=O)N1CC[C@@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 14, 20, 14, 14, 14, 10, 14, 10, 10, 10, 10, 10, 5, 2, 7, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 10, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 10, 10, 10, 10, 10, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 14, 14] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/319 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001449704760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449704760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449704760 none CC(C)(C)OC(=O)N1CC[C@@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 22, 14, 14, 14, 10, 14, 10, 10, 10, 10, 10, 4, 2, 6, 1, 1, 1, 3, 3, 6, 6, 3, 6, 6, 6, 10, 14, 30, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 14, 10, 10, 10, 10, 10, 10, 3, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 14, 14] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 105 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449704760 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760 Building ZINC001449704760 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449704760 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 318) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001449704760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449704760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449704760 none CC(C)(C)OC(=O)N1CC[C@@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 14, 20, 14, 14, 14, 10, 14, 10, 10, 10, 10, 10, 5, 2, 7, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 10, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 10, 10, 10, 10, 10, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 14, 14] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 319) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001449704760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449704760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449704760 none CC(C)(C)OC(=O)N1CC[C@@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 22, 14, 14, 14, 10, 14, 10, 10, 10, 10, 10, 4, 2, 6, 1, 1, 1, 3, 3, 6, 6, 3, 6, 6, 6, 10, 14, 30, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 14, 10, 10, 10, 10, 10, 10, 3, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 14, 14] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 105 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449704760 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704760 Building ZINC001449704762 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449704762 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/320 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001449704762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449704762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449704762 none CC(C)(C)OC(=O)N1CC[C@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 22, 14, 14, 14, 7, 14, 7, 8, 7, 7, 7, 4, 2, 6, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 7, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 7, 7, 7, 7, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/321 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001449704762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449704762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449704762 none CC(C)(C)OC(=O)N1CC[C@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 31, 31, 22, 13, 22, 13, 13, 13, 7, 13, 7, 9, 7, 7, 7, 4, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 7, 13, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 13, 13, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 13, 13] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449704762 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762 Building ZINC001449704762 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449704762 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 320) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001449704762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449704762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449704762 none CC(C)(C)OC(=O)N1CC[C@H]([C@@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 22, 14, 14, 14, 7, 14, 7, 8, 7, 7, 7, 4, 2, 6, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 7, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 7, 7, 7, 7, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 321) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001449704762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449704762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449704762 none CC(C)(C)OC(=O)N1CC[C@H]([C@@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 31, 31, 22, 13, 22, 13, 13, 13, 7, 13, 7, 9, 7, 7, 7, 4, 2, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 7, 13, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 13, 13, 13, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 13, 13] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449704762 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704762 Building ZINC001449704765 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449704765 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/322 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001449704765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449704765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449704765 none CC(C)(C)OC(=O)N1CC[C@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 23, 14, 23, 14, 14, 14, 9, 14, 9, 9, 9, 9, 9, 3, 2, 6, 1, 1, 1, 4, 4, 7, 7, 4, 7, 7, 7, 9, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 9, 9, 9, 9, 9, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 14, 14] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 106 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/323 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001449704765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449704765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449704765 none CC(C)(C)OC(=O)N1CC[C@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 22, 16, 22, 16, 16, 16, 10, 16, 10, 10, 10, 10, 10, 5, 2, 7, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 10, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 16, 16, 16, 10, 10, 10, 10, 10, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 16, 16] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 94 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449704765 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765 Building ZINC001449704765 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001449704765 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 322) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001449704765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001449704765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449704765 none CC(C)(C)OC(=O)N1CC[C@H]([C@H]2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 23, 14, 23, 14, 14, 14, 9, 14, 9, 9, 9, 9, 9, 3, 2, 6, 1, 1, 1, 4, 4, 7, 7, 4, 7, 7, 7, 9, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 9, 9, 9, 9, 9, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 14, 14] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 106 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 323) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1) `ZINC001449704765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001449704765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001449704765 none CC(C)(C)OC(=O)N1CC[C@H]([C@H]2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 22, 16, 22, 16, 16, 16, 10, 16, 10, 10, 10, 10, 10, 5, 2, 7, 1, 1, 1, 5, 5, 7, 7, 5, 7, 7, 7, 10, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16, 16, 16, 16, 10, 10, 10, 10, 10, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 16, 16] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 94 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001449704765 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001449704765 Building ZINC001450079312 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450079312 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/324 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccc3ccccc3n2)n[nH]1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001450079312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450079312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001450079312 none O=C(Nc1nc(c2ccc3ccccc3n2)n[nH]1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 7, 3, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 1, 1, 1, 10, 10, 10, 10, 10, 4, 28, 28, 28, 28, 28, 28, 10, 10] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/325 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccc3ccccc3n2)n[nH]1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001450079312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450079312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001450079312 none O=C(Nc1nc(c2ccc3ccccc3n2)n[nH]1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 7, 3, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 1, 1, 1, 10, 10, 10, 10, 10, 5, 30, 30, 30, 30, 30, 30, 10, 10] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001450079312 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312 Building ZINC001450079312 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450079312 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 324) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccc3ccccc3n2)n[nH]1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001450079312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450079312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001450079312 none O=C(Nc1nc(c2ccc3ccccc3n2)n[nH]1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 7, 3, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 1, 1, 1, 10, 10, 10, 10, 10, 4, 28, 28, 28, 28, 28, 28, 10, 10] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 325) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nc(c2ccc3ccccc3n2)n[nH]1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001450079312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450079312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001450079312 none O=C(Nc1nc(c2ccc3ccccc3n2)n[nH]1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 6, 5, 12, 1, 1, 1, 1, 17, 14, 6, 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, 7, 3, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 1, 1, 1, 10, 10, 10, 10, 10, 5, 30, 30, 30, 30, 30, 30, 10, 10] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001450079312 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450079312 Building ZINC001450833563 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450833563 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/326 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001450833563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450833563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001450833563 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C[C@@H]1CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 14, 29, 40, 40, 43, 43, 43, 43, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 14, 14, 29, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/327 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001450833563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450833563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001450833563 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C[C@@H]1CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 23, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001450833563 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563 Building ZINC001450833563 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450833563 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 326) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001450833563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450833563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001450833563 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C[C@@H]1CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 14, 29, 40, 40, 43, 43, 43, 43, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 14, 14, 29, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 327) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001450833563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450833563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001450833563 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C[C@@H]1CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 23, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001450833563 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833563 Building ZINC001450833565 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450833565 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/328 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001450833565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450833565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001450833565 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C[C@H]1CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 21, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 21, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/329 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001450833565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450833565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001450833565 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C[C@H]1CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 6, 2, 4, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 8, 15, 28, 38, 38, 42, 43, 43, 43, 8, 8, 8, 8, 8, 8, 8, 3, 3, 8, 8, 15, 15, 28, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001450833565 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565 Building ZINC001450833565 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450833565 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 328) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001450833565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450833565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001450833565 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C[C@H]1CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 2, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 21, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 21, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 329) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001450833565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450833565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001450833565 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C[C@H]1CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 6, 2, 4, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 8, 15, 28, 38, 38, 42, 43, 43, 43, 8, 8, 8, 8, 8, 8, 8, 3, 3, 8, 8, 15, 15, 28, 43, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001450833565 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833565 Building ZINC001450833568 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450833568 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/330 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001450833568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450833568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001450833568 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C[C@@H]1CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 5, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 6, 16, 33, 44, 44, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 2, 2, 6, 6, 16, 16, 33, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/331 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001450833568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450833568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001450833568 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C[C@@H]1CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 14, 26, 33, 33, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 2, 2, 4, 4, 14, 14, 26, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001450833568 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568 Building ZINC001450833568 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450833568 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 330) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001450833568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450833568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001450833568 none C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C[C@@H]1CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 5, 2, 5, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 6, 16, 33, 44, 44, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 2, 2, 6, 6, 16, 16, 33, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 331) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C[C@@H]1CNC(=O)OC(C)(C)C) `ZINC001450833568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450833568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001450833568 none C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C[C@@H]1CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 14, 26, 33, 33, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 2, 2, 4, 4, 14, 14, 26, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001450833568 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833568 Building ZINC001450833571 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450833571 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/332 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001450833571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450833571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001450833571 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C[C@H]1CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 12, 23, 31, 31, 39, 39, 39, 39, 4, 4, 4, 4, 4, 4, 4, 2, 2, 4, 4, 12, 12, 23, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/333 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001450833571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450833571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001450833571 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C[C@H]1CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 3, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 16, 27, 38, 38, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 5, 4, 4, 5, 5, 16, 16, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001450833571 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571 Building ZINC001450833571 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001450833571 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 332) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001450833571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001450833571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001450833571 none C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C[C@H]1CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 12, 23, 31, 31, 39, 39, 39, 39, 4, 4, 4, 4, 4, 4, 4, 2, 2, 4, 4, 12, 12, 23, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 333) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C[C@H]1CNC(=O)OC(C)(C)C) `ZINC001450833571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001450833571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001450833571 none C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C[C@H]1CNC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'C.3', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 3, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 16, 27, 38, 38, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 5, 4, 4, 5, 5, 16, 16, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001450833571 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001450833571 Building ZINC001451144434 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451144434 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/334 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)cc1Cl) `ZINC001451144434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451144434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001451144434 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)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', '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.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 5, 5, 5, 9, 9, 9, 5, 5, 2, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 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, 58]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/335 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)cc1Cl) `ZINC001451144434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451144434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001451144434 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)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', '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.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 5, 5, 5, 10, 10, 10, 5, 5, 2, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 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, 58]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001451144434 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434 Building ZINC001451144434 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451144434 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 334) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)cc1Cl) `ZINC001451144434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451144434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001451144434 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)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', '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.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 5, 5, 5, 9, 9, 9, 5, 5, 2, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 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, 58]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 335) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)cc1Cl) `ZINC001451144434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451144434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001451144434 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)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', '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.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 5, 5, 5, 10, 10, 10, 5, 5, 2, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 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, 58]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001451144434 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144434 Building ZINC001451144448 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451144448 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/336 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)cc1Cl) `ZINC001451144448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451144448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001451144448 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)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', '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.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 13, 13, 13, 13, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 6, 6, 3, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 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, 58]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/337 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)cc1Cl) `ZINC001451144448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451144448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001451144448 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)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', '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.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 15, 15, 15, 15, 7, 7, 7, 7, 6, 6, 6, 11, 11, 11, 6, 6, 3, 7, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 7, 7, 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, 58]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001451144448 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448 Building ZINC001451144448 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451144448 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 336) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)cc1Cl) `ZINC001451144448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451144448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001451144448 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)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', '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.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 13, 13, 13, 13, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 6, 6, 3, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 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, 58]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 337) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)cc1Cl) `ZINC001451144448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451144448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001451144448 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)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', '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.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 15, 15, 15, 15, 7, 7, 7, 7, 6, 6, 6, 11, 11, 11, 6, 6, 3, 7, 7, 7, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 7, 7, 7, 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, 58]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001451144448 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144448 Building ZINC001451144460 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451144460 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/338 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CN(C(=O)OC(C)(C)C)C[C@@H]3C2)cc1Cl) `ZINC001451144460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451144460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001451144460 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CN(C(=O)OC(C)(C)C)C[C@@H]3C2)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', '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.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 18, 18, 18, 18, 9, 9, 9, 9, 6, 6, 6, 11, 11, 11, 6, 6, 3, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 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, 58]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/339 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CN(C(=O)OC(C)(C)C)C[C@@H]3C2)cc1Cl) `ZINC001451144460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451144460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001451144460 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CN(C(=O)OC(C)(C)C)C[C@@H]3C2)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', '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.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 18, 18, 18, 18, 11, 11, 11, 11, 6, 6, 6, 13, 13, 13, 6, 6, 3, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 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, 58]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001451144460 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460 Building ZINC001451144460 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451144460 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 338) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)N[C@@H]2CC[C@H]3CN(C(=O)OC(C)(C)C)C[C@@H]3C2)cc1Cl) `ZINC001451144460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451144460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001451144460 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CN(C(=O)OC(C)(C)C)C[C@@H]3C2)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', '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.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 18, 18, 18, 18, 9, 9, 9, 9, 6, 6, 6, 11, 11, 11, 6, 6, 3, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 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, 58]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 339) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)N[C@@H]2CC[C@H]3CN(C(=O)OC(C)(C)C)C[C@@H]3C2)cc1Cl) `ZINC001451144460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451144460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001451144460 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@H]3CN(C(=O)OC(C)(C)C)C[C@@H]3C2)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', '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.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 4, 11, 11, 11, 11, 11, 11, 11, 11, 17, 17, 18, 18, 18, 18, 11, 11, 11, 11, 6, 6, 6, 13, 13, 13, 6, 6, 3, 11, 11, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 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, 58]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001451144460 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144460 Building ZINC001451144467 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451144467 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/340 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(C(=O)OC(C)(C)C)C[C@@H]3C2)cc1Cl) `ZINC001451144467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451144467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001451144467 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(C(=O)OC(C)(C)C)C[C@@H]3C2)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', '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.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 11, 11, 11, 11, 6, 6, 6, 10, 10, 10, 6, 6, 3, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 11, 11, 11, 11, 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, 58]) total number of confs: 75 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/341 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(C(=O)OC(C)(C)C)C[C@@H]3C2)cc1Cl) `ZINC001451144467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451144467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001451144467 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(C(=O)OC(C)(C)C)C[C@@H]3C2)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', '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.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 19, 19, 19, 19, 9, 9, 9, 9, 6, 6, 6, 10, 10, 10, 6, 6, 3, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 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, 58]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001451144467 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467 Building ZINC001451144467 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451144467 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 340) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(C(=O)OC(C)(C)C)C[C@@H]3C2)cc1Cl) `ZINC001451144467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451144467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001451144467 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(C(=O)OC(C)(C)C)C[C@@H]3C2)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', '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.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 11, 11, 11, 11, 6, 6, 6, 10, 10, 10, 6, 6, 3, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 11, 11, 11, 11, 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, 58]) total number of confs: 75 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 341) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(C(=O)OC(C)(C)C)C[C@@H]3C2)cc1Cl) `ZINC001451144467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451144467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001451144467 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CC[C@@H]3CN(C(=O)OC(C)(C)C)C[C@@H]3C2)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', '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.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', '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, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 19, 19, 19, 19, 9, 9, 9, 9, 6, 6, 6, 10, 10, 10, 6, 6, 3, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 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, 58]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001451144467 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451144467 Building ZINC001451390790 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451390790 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/342 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2cccc(F)c2)[C@H](NC(=O)OC(C)(C)C)C1) `ZINC001451390790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451390790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001451390790 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2cccc(F)c2)[C@H](NC(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 15, 1, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 6, 6, 6, 16, 23, 23, 30, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 6] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 7, 8, 9, 10, 39, 2, 3, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/343 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2cccc(F)c2)[C@H](NC(=O)OC(C)(C)C)C1) `ZINC001451390790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451390790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001451390790 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2cccc(F)c2)[C@H](NC(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 15, 1, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 7, 7, 7, 18, 26, 26, 28, 28, 28, 28, 7, 1, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 7, 8, 9, 10, 39, 2, 3, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001451390790 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790 Building ZINC001451390790 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451390790 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 342) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2cccc(F)c2)[C@H](NC(=O)OC(C)(C)C)C1) `ZINC001451390790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451390790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001451390790 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2cccc(F)c2)[C@H](NC(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 15, 1, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 6, 6, 6, 16, 23, 23, 30, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30, 6, 6] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 7, 8, 9, 10, 39, 2, 3, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 343) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2cccc(F)c2)[C@H](NC(=O)OC(C)(C)C)C1) `ZINC001451390790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451390790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001451390790 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2cccc(F)c2)[C@H](NC(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 15, 1, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 7, 7, 7, 18, 26, 26, 28, 28, 28, 28, 7, 1, 1, 1, 1, 1, 1, 7, 7, 16, 16, 16, 16, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 7, 8, 9, 10, 39, 2, 3, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001451390790 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451390790 Building ZINC001451405348 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451405348 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/344 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(F)c3)[C@H](NC(=O)OC(C)(C)C)C2)c1) `ZINC001451405348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451405348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001451405348 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(F)c3)[C@H](NC(=O)OC(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 3, 9, 13, 13, 19, 19, 19, 19, 3, 2, 2, 2, 2, 2, 2, 2, 3, 3, 5, 5, 5, 5, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 2] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/345 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(F)c3)[C@H](NC(=O)OC(C)(C)C)C2)c1) `ZINC001451405348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451405348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001451405348 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(F)c3)[C@H](NC(=O)OC(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 4, 4, 4, 10, 14, 14, 14, 14, 14, 14, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 8, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001451405348 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348 Building ZINC001451405348 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451405348 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 344) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(F)c3)[C@H](NC(=O)OC(C)(C)C)C2)c1) `ZINC001451405348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451405348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001451405348 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(F)c3)[C@H](NC(=O)OC(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3, 3, 9, 13, 13, 19, 19, 19, 19, 3, 2, 2, 2, 2, 2, 2, 2, 3, 3, 5, 5, 5, 5, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 3, 2] 50 rigid atoms, others: [8, 9, 5, 6, 7] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 345) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(F)c3)[C@H](NC(=O)OC(C)(C)C)C2)c1) `ZINC001451405348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451405348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001451405348 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3cccc(F)c3)[C@H](NC(=O)OC(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 4, 4, 4, 10, 14, 14, 14, 14, 14, 14, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 8, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001451405348 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451405348 Building ZINC001451408990 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451408990 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/346 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2F)[C@H](NC(=O)OC(C)(C)C)C1) `ZINC001451408990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451408990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001451408990 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2F)[C@H](NC(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 15, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 9, 9, 8, 9, 9, 9, 6, 6, 6, 19, 30, 30, 38, 38, 38, 38, 6, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 19, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 7, 8, 9, 10, 39, 2, 3, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/347 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2F)[C@H](NC(=O)OC(C)(C)C)C1) `ZINC001451408990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451408990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001451408990 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2F)[C@H](NC(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 15, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 17, 17, 10, 17, 17, 17, 8, 8, 8, 18, 31, 31, 33, 33, 33, 33, 8, 1, 1, 1, 1, 1, 1, 8, 8, 17, 17, 17, 17, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 7, 8, 9, 10, 39, 2, 3, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 131 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001451408990 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990 Building ZINC001451408990 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451408990 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 346) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2F)[C@H](NC(=O)OC(C)(C)C)C1) `ZINC001451408990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451408990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001451408990 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2F)[C@H](NC(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 15, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 9, 9, 8, 9, 9, 9, 6, 6, 6, 19, 30, 30, 38, 38, 38, 38, 6, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 19, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 7, 8, 9, 10, 39, 2, 3, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 347) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2F)[C@H](NC(=O)OC(C)(C)C)C1) `ZINC001451408990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451408990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001451408990 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2F)[C@H](NC(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 15, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 17, 17, 10, 17, 17, 17, 8, 8, 8, 18, 31, 31, 33, 33, 33, 33, 8, 1, 1, 1, 1, 1, 1, 8, 8, 17, 17, 17, 17, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 7, 8, 9, 10, 39, 2, 3, 4, 6, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 131 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001451408990 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451408990 Building ZINC001451412735 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451412735 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/348 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3F)[C@H](NC(=O)OC(C)(C)C)C2)c1) `ZINC001451412735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451412735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001451412735 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3F)[C@H](NC(=O)OC(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 20, 20, 28, 28, 28, 28, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/349 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3F)[C@H](NC(=O)OC(C)(C)C)C2)c1) `ZINC001451412735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451412735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001451412735 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3F)[C@H](NC(=O)OC(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 7, 7, 6, 7, 7, 7, 4, 4, 4, 12, 19, 19, 19, 19, 19, 19, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 7, 7, 7, 7, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001451412735 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735 Building ZINC001451412735 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001451412735 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 348) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3F)[C@H](NC(=O)OC(C)(C)C)C2)c1) `ZINC001451412735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001451412735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001451412735 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3F)[C@H](NC(=O)OC(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 20, 20, 28, 28, 28, 28, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 349) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3F)[C@H](NC(=O)OC(C)(C)C)C2)c1) `ZINC001451412735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001451412735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001451412735 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](c3ccccc3F)[C@H](NC(=O)OC(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 15, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 7, 7, 6, 7, 7, 7, 4, 4, 4, 12, 19, 19, 19, 19, 19, 19, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 7, 7, 7, 7, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001451412735 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001451412735 Building ZINC001452162565 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452162565 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/350 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C1CC1) `ZINC001452162565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452162565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001452162565 none CC(C)(C)OC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 46, 33, 46, 18, 12, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 33, 33, 33, 47, 47, 47, 47, 47, 47, 47, 47, 47, 18, 18, 16, 16, 11, 11, 2, 4, 4, 33, 33, 33, 33, 33] 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: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/351 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C1CC1) `ZINC001452162565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452162565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001452162565 none CC(C)(C)OC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 46, 32, 46, 17, 12, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 32, 32, 32, 47, 47, 47, 47, 47, 47, 47, 47, 47, 17, 17, 15, 15, 11, 11, 2, 4, 4, 32, 32, 32, 32, 32] 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: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001452162565 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565 Building ZINC001452162565 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452162565 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 350) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C1CC1) `ZINC001452162565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452162565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001452162565 none CC(C)(C)OC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 46, 33, 46, 18, 12, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 33, 33, 33, 47, 47, 47, 47, 47, 47, 47, 47, 47, 18, 18, 16, 16, 11, 11, 2, 4, 4, 33, 33, 33, 33, 33] 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: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 351) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C1CC1) `ZINC001452162565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452162565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001452162565 none CC(C)(C)OC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 46, 32, 46, 17, 12, 11, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 32, 32, 32, 47, 47, 47, 47, 47, 47, 47, 47, 47, 17, 17, 15, 15, 11, 11, 2, 4, 4, 32, 32, 32, 32, 32] 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: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001452162565 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452162565 Building ZINC001452499104 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452499104 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/352 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCc1nc(c2ccccn2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001452499104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452499104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001452499104 none O=C(NCCCCc1nc(c2ccccn2)cs1)[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', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 13, 14, 17, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 14, 14, 14, 14, 17, 17, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3] 50 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/353 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCc1nc(c2ccccn2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001452499104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452499104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001452499104 none O=C(NCCCCc1nc(c2ccccn2)cs1)[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', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 13, 14, 16, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 14, 14, 14, 14, 16, 16, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4] 50 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001452499104 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104 Building ZINC001452499104 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452499104 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 352) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCCCCc1nc(c2ccccn2)cs1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001452499104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452499104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001452499104 none O=C(NCCCCc1nc(c2ccccn2)cs1)[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', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 13, 14, 17, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 14, 14, 14, 14, 17, 17, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3] 50 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 353) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCCCCc1nc(c2ccccn2)cs1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001452499104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452499104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001452499104 none O=C(NCCCCc1nc(c2ccccn2)cs1)[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', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'S.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 13, 14, 16, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 14, 14, 14, 14, 16, 16, 45, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4] 50 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001452499104 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452499104 Building ZINC001452801584 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452801584 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/354 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)Cc2ccccc21) `ZINC001452801584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452801584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001452801584 none CC(C)(C)OC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 28, 29, 28, 28, 7, 26, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 28, 28, 3, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28] 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/355 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)Cc2ccccc21) `ZINC001452801584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452801584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001452801584 none CC(C)(C)OC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 7, 29, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 35, 35, 35, 35, 35, 35, 35, 35, 35, 31, 31, 3, 4, 4, 4, 4, 31, 31, 31, 31, 31, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001452801584 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584 Building ZINC001452801584 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452801584 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 354) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)Cc2ccccc21) `ZINC001452801584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452801584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001452801584 none CC(C)(C)OC(=O)N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 28, 29, 28, 28, 7, 26, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 32, 32, 32, 32, 32, 32, 32, 32, 32, 28, 28, 3, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28] 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 355) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)Cc2ccccc21) `ZINC001452801584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452801584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001452801584 none CC(C)(C)OC(=O)N1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 31, 7, 29, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 35, 35, 35, 35, 35, 35, 35, 35, 35, 31, 31, 3, 4, 4, 4, 4, 31, 31, 31, 31, 31, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001452801584 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801584 Building ZINC001452801593 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452801593 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/356 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)Cc2ccccc21) `ZINC001452801593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452801593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001452801593 none CC(C)(C)OC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 31, 30, 31, 30, 30, 7, 29, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 36, 36, 36, 36, 36, 36, 36, 36, 36, 30, 30, 3, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30] 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: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/357 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)Cc2ccccc21) `ZINC001452801593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452801593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001452801593 none CC(C)(C)OC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 33, 31, 33, 31, 31, 7, 30, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 37, 37, 37, 37, 37, 37, 37, 37, 37, 31, 31, 3, 4, 4, 4, 4, 31, 31, 31, 31, 31, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001452801593 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593 Building ZINC001452801593 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452801593 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 356) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)Cc2ccccc21) `ZINC001452801593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452801593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001452801593 none CC(C)(C)OC(=O)N1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 31, 30, 31, 30, 30, 7, 29, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 36, 36, 36, 36, 36, 36, 36, 36, 36, 30, 30, 3, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30] 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: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 357) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)Cc2ccccc21) `ZINC001452801593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452801593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001452801593 none CC(C)(C)OC(=O)N1C[C@H](NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)Cc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 33, 31, 33, 31, 31, 7, 30, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 37, 37, 37, 37, 37, 37, 37, 37, 37, 31, 31, 3, 4, 4, 4, 4, 31, 31, 31, 31, 31, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001452801593 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452801593 Building ZINC001452803808 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452803808 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/358 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c(F)c1) `ZINC001452803808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452803808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001452803808 none CC(C)(C)OC(=O)NCc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 27, 36, 22, 13, 9, 13, 13, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 36, 36, 36, 36, 36, 36, 36, 36, 36, 27, 22, 22, 13, 13, 8, 8, 3, 4, 4, 4, 4, 13] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/359 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c(F)c1) `ZINC001452803808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452803808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001452803808 none CC(C)(C)OC(=O)NCc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 28, 37, 23, 13, 9, 13, 13, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 28, 23, 23, 13, 13, 8, 8, 3, 3, 3, 3, 3, 13] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001452803808 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808 Building ZINC001452803808 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001452803808 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 358) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c(F)c1) `ZINC001452803808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001452803808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001452803808 none CC(C)(C)OC(=O)NCc1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 27, 36, 22, 13, 9, 13, 13, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 36, 36, 36, 36, 36, 36, 36, 36, 36, 27, 22, 22, 13, 13, 8, 8, 3, 4, 4, 4, 4, 13] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 359) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c(F)c1) `ZINC001452803808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001452803808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001452803808 none CC(C)(C)OC(=O)NCc1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 28, 37, 23, 13, 9, 13, 13, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 28, 23, 23, 13, 13, 8, 8, 3, 3, 3, 3, 3, 13] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001452803808 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001452803808 Building ZINC001453071231 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453071231 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/360 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)on2)cc1) `ZINC001453071231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453071231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001453071231 none COc1ccc(c2cc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)on2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', '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', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 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: [43, 24, 24, 43, 43, 24, 24, 24, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 24, 24, 43, 43, 43, 43, 43, 43, 43, 24, 10, 10, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 43, 43] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/361 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)on2)cc1) `ZINC001453071231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453071231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001453071231 none COc1ccc(c2cc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)on2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', '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', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 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: [44, 23, 23, 44, 44, 23, 23, 23, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 23, 23, 44, 44, 44, 44, 44, 44, 44, 23, 10, 10, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 44, 44] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453071231 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231 Building ZINC001453071231 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453071231 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 360) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc(c2cc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)on2)cc1) `ZINC001453071231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453071231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001453071231 none COc1ccc(c2cc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)on2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', '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', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 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: [43, 24, 24, 43, 43, 24, 24, 24, 10, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 24, 24, 43, 43, 43, 43, 43, 43, 43, 24, 10, 10, 2, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 43, 43] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 361) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc(c2cc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)on2)cc1) `ZINC001453071231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453071231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001453071231 none COc1ccc(c2cc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)on2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', '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', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 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: [44, 23, 23, 44, 44, 23, 23, 23, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 23, 23, 44, 44, 44, 44, 44, 44, 44, 23, 10, 10, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 44, 44] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453071231 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453071231 Building ZINC001453145133 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453145133 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/362 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2C1) `ZINC001453145133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453145133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001453145133 none CC(C)(C)OC(=O)N1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 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, 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] 0 hydrogens 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, 18, 12, 18, 12, 12, 11, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12, 12, 3, 6, 7, 7, 6, 7, 7, 6, 12, 12] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/363 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2C1) `ZINC001453145133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453145133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001453145133 none CC(C)(C)OC(=O)N1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 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, 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] 0 hydrogens 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, 17, 11, 17, 11, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 11, 11, 11, 11, 2, 7, 8, 8, 7, 8, 8, 7, 11, 11] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453145133 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133 Building ZINC001453145133 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453145133 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 362) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2C1) `ZINC001453145133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453145133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001453145133 none CC(C)(C)OC(=O)N1Cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 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, 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] 0 hydrogens 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, 18, 12, 18, 12, 12, 11, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12, 12, 3, 6, 7, 7, 6, 7, 7, 6, 12, 12] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 363) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2C1) `ZINC001453145133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453145133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001453145133 none CC(C)(C)OC(=O)N1Cc2cccc(NC(=O)[C@]([O-])([SiH3])c3cnn(c4ccccc4)c3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 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, 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] 0 hydrogens 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, 17, 11, 17, 11, 11, 11, 11, 11, 11, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 25, 11, 11, 11, 11, 11, 2, 7, 8, 8, 7, 8, 8, 7, 11, 11] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453145133 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453145133 Building ZINC001453282916 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453282916 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/364 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2Cc3ccccc3[C@@H](C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001453282916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453282916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001453282916 none COc1ccc([C@]([O-])([SiH3])C(=O)N2Cc3ccccc3[C@@H](C(=O)OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', '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, 7, 1, 11, 12, 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, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 3, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 28, 28, 28, 28, 4, 3, 3, 3, 6, 6, 6, 3, 3, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 3] 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, 49, 50, 51, 52, 53]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/365 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2Cc3ccccc3[C@@H](C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001453282916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453282916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001453282916 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2Cc3ccccc3[C@@H](C(=O)OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', '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, 7, 1, 11, 12, 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, 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, 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, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 27, 27, 27, 27, 4, 2, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 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, 48, 49, 50, 51, 52, 53]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453282916 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916 Building ZINC001453282916 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453282916 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 364) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2Cc3ccccc3[C@@H](C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001453282916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453282916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001453282916 none COc1ccc([C@]([O-])([SiH3])C(=O)N2Cc3ccccc3[C@@H](C(=O)OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', '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, 7, 1, 11, 12, 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, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 3, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 28, 28, 28, 28, 4, 3, 3, 3, 6, 6, 6, 3, 3, 4, 4, 4, 4, 4, 4, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 3] 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, 49, 50, 51, 52, 53]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 365) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2Cc3ccccc3[C@@H](C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001453282916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453282916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001453282916 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2Cc3ccccc3[C@@H](C(=O)OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', '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, 7, 1, 11, 12, 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, 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, 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, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 27, 27, 27, 27, 4, 2, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 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, 48, 49, 50, 51, 52, 53]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453282916 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282916 Building ZINC001453282939 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453282939 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/366 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2Cc3ccccc3[C@H](C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001453282939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453282939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001453282939 none COc1ccc([C@]([O-])([SiH3])C(=O)N2Cc3ccccc3[C@H](C(=O)OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', '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, 7, 1, 11, 12, 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, 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, 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, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 26, 26, 26, 26, 4, 2, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 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, 48, 49, 50, 51, 52, 53]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/367 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2Cc3ccccc3[C@H](C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001453282939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453282939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001453282939 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2Cc3ccccc3[C@H](C(=O)OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', '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, 7, 1, 11, 12, 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, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 3, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 27, 27, 27, 27, 4, 3, 3, 3, 6, 6, 6, 3, 3, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 3] 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, 49, 50, 51, 52, 53]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453282939 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939 Building ZINC001453282939 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453282939 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 366) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2Cc3ccccc3[C@H](C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001453282939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453282939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001453282939 none COc1ccc([C@]([O-])([SiH3])C(=O)N2Cc3ccccc3[C@H](C(=O)OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', '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, 7, 1, 11, 12, 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, 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, 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, 7] 0 hydrogens need 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, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 26, 26, 26, 26, 4, 2, 2, 2, 4, 4, 4, 2, 2, 4, 4, 4, 4, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 4, 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, 48, 49, 50, 51, 52, 53]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 367) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2Cc3ccccc3[C@H](C(=O)OC(C)(C)C)C2)cc1Cl) `ZINC001453282939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453282939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001453282939 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2Cc3ccccc3[C@H](C(=O)OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', '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, 7, 1, 11, 12, 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, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 3, 3, 3, 3, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 27, 27, 27, 27, 4, 3, 3, 3, 6, 6, 6, 3, 3, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 3] 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, 49, 50, 51, 52, 53]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453282939 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453282939 Building ZINC001453359756 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453359756 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/368 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]12CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C[C@H]1C2(Br)Br) `ZINC001453359756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453359756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001453359756 none C[C@]12CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C[C@H]1C2(Br)Br NO_LONG_NAME dock atom types: ['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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'Br', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 11, 2, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 21, 21] 21 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/369 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]12CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C[C@H]1C2(Br)Br) `ZINC001453359756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453359756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001453359756 none C[C@]12CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C[C@H]1C2(Br)Br NO_LONG_NAME dock atom types: ['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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'Br', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 25, 25, 25, 13, 2, 13, 1, 1, 1, 5, 5, 1, 1, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 25, 25] 30 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]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453359756 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756 Building ZINC001453359756 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453359756 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 368) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@]12CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C[C@H]1C2(Br)Br) `ZINC001453359756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453359756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001453359756 none C[C@]12CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C[C@H]1C2(Br)Br NO_LONG_NAME dock atom types: ['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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'Br', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 11, 2, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 3, 3, 3, 21, 21] 21 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 369) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@]12CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C[C@H]1C2(Br)Br) `ZINC001453359756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453359756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001453359756 none C[C@]12CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C[C@H]1C2(Br)Br NO_LONG_NAME dock atom types: ['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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'Br', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 25, 25, 25, 13, 2, 13, 1, 1, 1, 5, 5, 1, 1, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 25, 25] 30 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]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453359756 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453359756 Building ZINC001453536718 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453536718 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/370 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC[C@H]1C(F)(F)F) `ZINC001453536718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453536718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001453536718 none CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 30, 40, 11, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 11, 11, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [48, 49, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/371 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC[C@H]1C(F)(F)F) `ZINC001453536718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453536718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001453536718 none CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 31, 44, 10, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 10, 10, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453536718 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718 Building ZINC001453536718 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453536718 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 370) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC[C@H]1C(F)(F)F) `ZINC001453536718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453536718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001453536718 none CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 30, 40, 11, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 11, 11, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [48, 49, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 371) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC[C@H]1C(F)(F)F) `ZINC001453536718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453536718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001453536718 none CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 31, 44, 10, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 10, 10, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453536718 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536718 Building ZINC001453536726 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453536726 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/372 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC[C@@H]1C(F)(F)F) `ZINC001453536726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453536726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001453536726 none CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 34, 48, 12, 6, 6, 6, 6, 4, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 12, 12, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/373 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC[C@@H]1C(F)(F)F) `ZINC001453536726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453536726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001453536726 none CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 32, 42, 12, 7, 7, 7, 7, 5, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 12, 12, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453536726 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726 Building ZINC001453536726 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453536726 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 372) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC[C@@H]1C(F)(F)F) `ZINC001453536726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453536726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001453536726 none CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 34, 48, 12, 6, 6, 6, 6, 4, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 12, 12, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 373) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC[C@@H]1C(F)(F)F) `ZINC001453536726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453536726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001453536726 none CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 32, 42, 12, 7, 7, 7, 7, 5, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 12, 12, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453536726 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536726 Building ZINC001453536735 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453536735 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/374 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC[C@H]1C(F)(F)F) `ZINC001453536735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453536735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001453536735 none CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 28, 40, 12, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 49, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/375 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC[C@H]1C(F)(F)F) `ZINC001453536735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453536735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001453536735 none CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 33, 44, 18, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 18, 18, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453536735 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735 Building ZINC001453536735 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453536735 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 374) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC[C@H]1C(F)(F)F) `ZINC001453536735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453536735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001453536735 none CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 28, 40, 12, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 49, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 375) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC[C@H]1C(F)(F)F) `ZINC001453536735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453536735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001453536735 none CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 33, 44, 18, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 18, 18, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453536735 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536735 Building ZINC001453536742 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453536742 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/376 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC[C@@H]1C(F)(F)F) `ZINC001453536742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453536742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001453536742 none CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 50, 23, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 23, 23, 8, 8, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/377 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC[C@@H]1C(F)(F)F) `ZINC001453536742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453536742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001453536742 none CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 37, 49, 22, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 22, 22, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453536742 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742 Building ZINC001453536742 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453536742 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 376) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)OC(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC[C@@H]1C(F)(F)F) `ZINC001453536742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453536742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001453536742 none CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 39, 50, 23, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 23, 23, 8, 8, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 377) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)OC(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC[C@@H]1C(F)(F)F) `ZINC001453536742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453536742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001453536742 none CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 37, 49, 22, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 22, 22, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [48, 49, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 50, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453536742 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453536742 Building ZINC001453567827 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453567827 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/378 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C(=O)OC(C)(C)C) `ZINC001453567827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453567827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001453567827 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 19, 17, 10, 5, 5, 3, 2, 3, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 38, 38, 50, 50, 50, 50, 30, 30, 30, 19, 19, 17, 17, 5, 5, 5, 5, 3, 3, 3, 3, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/379 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C(=O)OC(C)(C)C) `ZINC001453567827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453567827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001453567827 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 17, 10, 5, 5, 3, 2, 3, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 29, 39, 39, 50, 50, 50, 50, 29, 29, 29, 20, 20, 17, 17, 5, 5, 5, 5, 3, 3, 3, 3, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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, 53]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453567827 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827 Building ZINC001453567827 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453567827 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 378) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C(=O)OC(C)(C)C) `ZINC001453567827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453567827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001453567827 none CN(CCOCCN(C)C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 19, 17, 10, 5, 5, 3, 2, 3, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 30, 38, 38, 50, 50, 50, 50, 30, 30, 30, 19, 19, 17, 17, 5, 5, 5, 5, 3, 3, 3, 3, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 379) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C(=O)OC(C)(C)C) `ZINC001453567827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453567827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001453567827 none CN(CCOCCN(C)C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', '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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 17, 10, 5, 5, 3, 2, 3, 1, 2, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 29, 39, 39, 50, 50, 50, 50, 29, 29, 29, 20, 20, 17, 17, 5, 5, 5, 5, 3, 3, 3, 3, 1, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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, 53]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453567827 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453567827 Building ZINC001453731970 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453731970 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/380 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NC2CCN(C(=O)Nc3ccc(Br)cc3)CC2)c1) `ZINC001453731970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453731970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001453731970 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NC2CCN(C(=O)Nc3ccc(Br)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 22, 22, 28, 28, 28, 28, 28, 28, 28, 14, 14, 4, 4, 4, 4, 2, 4, 4, 2, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 14, 14, 14, 14, 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, 48, 49]) total number of confs: 100 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/381 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NC2CCN(C(=O)Nc3ccc(Br)cc3)CC2)c1) `ZINC001453731970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453731970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001453731970 none Cc1cccc([C@]([O-])([SiH3])C(=O)NC2CCN(C(=O)Nc3ccc(Br)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 20, 20, 26, 26, 26, 26, 26, 26, 26, 14, 14, 4, 4, 4, 4, 2, 4, 4, 2, 14, 14, 14, 14, 14, 26, 26, 26, 26, 26, 14, 14, 14, 14, 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, 48, 49]) total number of confs: 92 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453731970 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970 Building ZINC001453731970 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453731970 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 380) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)NC2CCN(C(=O)Nc3ccc(Br)cc3)CC2)c1) `ZINC001453731970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453731970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001453731970 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NC2CCN(C(=O)Nc3ccc(Br)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 22, 22, 28, 28, 28, 28, 28, 28, 28, 14, 14, 4, 4, 4, 4, 2, 4, 4, 2, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 14, 14, 14, 14, 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, 48, 49]) total number of confs: 100 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 381) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@]([O-])([SiH3])C(=O)NC2CCN(C(=O)Nc3ccc(Br)cc3)CC2)c1) `ZINC001453731970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453731970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001453731970 none Cc1cccc([C@]([O-])([SiH3])C(=O)NC2CCN(C(=O)Nc3ccc(Br)cc3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 20, 20, 26, 26, 26, 26, 26, 26, 26, 14, 14, 4, 4, 4, 4, 2, 4, 4, 2, 14, 14, 14, 14, 14, 26, 26, 26, 26, 26, 14, 14, 14, 14, 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, 48, 49]) total number of confs: 92 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453731970 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453731970 Building ZINC001453862696 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453862696 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/382 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(c2noc(CC3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)CCCC1) `ZINC001453862696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453862696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001453862696 none COC1(c2noc(CC3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 27, 27, 27, 7, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 27, 50, 50, 50, 50, 50, 50, 50, 7, 7, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/383 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(c2noc(CC3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)CCCC1) `ZINC001453862696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453862696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001453862696 none COC1(c2noc(CC3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 24, 23, 23, 23, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453862696 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696 Building ZINC001453862696 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001453862696 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 382) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC1(c2noc(CC3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)CCCC1) `ZINC001453862696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001453862696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001453862696 none COC1(c2noc(CC3CCN(C(=O)[C@@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 28, 27, 27, 27, 7, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 27, 50, 50, 50, 50, 50, 50, 50, 7, 7, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 383) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC1(c2noc(CC3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)CCCC1) `ZINC001453862696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001453862696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001453862696 none COC1(c2noc(CC3CCN(C(=O)[C@]([O-])([SiH3])c4ccc(Cl)cc4)CC3)n2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 24, 23, 23, 23, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001453862696 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001453862696 Building ZINC001454241793 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454241793 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/384 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2Cc3cnn(c4ccccc4F)c3CC(C)(C)C2)cn1) `ZINC001454241793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454241793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001454241793 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2Cc3cnn(c4ccccc4F)c3CC(C)(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9, 9, 9, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 9, 9, 9, 28, 28, 28, 28, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/385 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2Cc3cnn(c4ccccc4F)c3CC(C)(C)C2)cn1) `ZINC001454241793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454241793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001454241793 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2Cc3cnn(c4ccccc4F)c3CC(C)(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 6, 4, 4, 1, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 7, 7, 7, 7, 7, 7, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 7, 28, 28, 28, 28, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001454241793 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793 Building ZINC001454241793 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454241793 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 384) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2Cc3cnn(c4ccccc4F)c3CC(C)(C)C2)cn1) `ZINC001454241793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454241793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001454241793 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2Cc3cnn(c4ccccc4F)c3CC(C)(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 6, 8, 9, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9, 9, 9, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 9, 9, 9, 28, 28, 28, 28, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 385) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2Cc3cnn(c4ccccc4F)c3CC(C)(C)C2)cn1) `ZINC001454241793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454241793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001454241793 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2Cc3cnn(c4ccccc4F)c3CC(C)(C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 6, 4, 4, 1, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 7, 7, 7, 7, 7, 7, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 7, 28, 28, 28, 28, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001454241793 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454241793 Building ZINC001454265624 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454265624 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/386 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/386' -> `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]2C(O)(c2ccccc2)c2ccccc2)cn1) `ZINC001454265624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454265624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001454265624 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2C(O)(c2ccccc2)c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 6, 6, 4, 4, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 11, 11, 11, 11, 11, 11, 36, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4] 54 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, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 81 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/387 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/387' -> `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]2C(O)(c2ccccc2)c2ccccc2)cn1) `ZINC001454265624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454265624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001454265624 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2C(O)(c2ccccc2)c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [13, 8, 13, 13, 8, 8, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 20, 20, 22, 22, 20, 22, 22, 20, 23, 23, 21, 23, 23, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 11, 11, 11, 11, 11, 11, 60, 22, 22, 20, 22, 22, 23, 23, 21, 23, 23, 8] 138 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, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 186 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001454265624 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624 Building ZINC001454265624 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454265624 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 386) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2C(O)(c2ccccc2)c2ccccc2)cn1) `ZINC001454265624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454265624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001454265624 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H]2C(O)(c2ccccc2)c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 6, 6, 4, 4, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 11, 11, 11, 11, 11, 11, 36, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4] 54 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, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 81 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 387) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2C(O)(c2ccccc2)c2ccccc2)cn1) `ZINC001454265624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454265624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001454265624 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H]2C(O)(c2ccccc2)c2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', '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, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [13, 8, 13, 13, 8, 8, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 20, 20, 22, 22, 20, 22, 22, 20, 23, 23, 21, 23, 23, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 11, 11, 11, 11, 11, 11, 60, 22, 22, 20, 22, 22, 23, 23, 21, 23, 23, 8] 138 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, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 186 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001454265624 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454265624 Building ZINC001454412827 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454412827 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/388 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)cc1c1nn[nH]n1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001454412827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001454412827 none O=C(Nc1ccc(Br)cc1c1nn[nH]n1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 8, 6, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 23, 23, 23, 23, 23, 23, 23, 37, 37, 37, 37, 37, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 6, 23, 23, 23, 5, 1, 5] 50 rigid atoms, others: [1, 16, 17, 18] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/389 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(Br)cc1c1nn[nH]n1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001454412827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001454412827 none O=C(Nc1ccc(Br)cc1c1nn[nH]n1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 8, 6, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 23, 23, 23, 23, 23, 23, 23, 37, 37, 37, 37, 37, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 6, 23, 23, 23, 5, 1, 5] 50 rigid atoms, others: [1, 16, 17, 18] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001454412827 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827 Building ZINC001454412827 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454412827 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 388) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(Nc1ccc(Br)cc1c1nn[nH]n1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001454412827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001454412827 none O=C(Nc1ccc(Br)cc1c1nn[nH]n1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 8, 6, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 23, 23, 23, 23, 23, 23, 23, 37, 37, 37, 37, 37, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 6, 23, 23, 23, 5, 1, 5] 50 rigid atoms, others: [1, 16, 17, 18] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 389) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(Nc1ccc(Br)cc1c1nn[nH]n1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001454412827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454412827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001454412827 none O=C(Nc1ccc(Br)cc1c1nn[nH]n1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 8, 8, 6, 8, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 23, 23, 23, 23, 23, 23, 23, 37, 37, 37, 37, 37, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 6, 23, 23, 23, 5, 1, 5] 50 rigid atoms, others: [1, 16, 17, 18] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001454412827 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454412827 Building ZINC001454502051 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454502051 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/390 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@@H](O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1) `ZINC001454502051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454502051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001454502051 none COc1cccc([C@@H](O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 1, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 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, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 34, 34, 13, 5, 13, 13, 5, 5, 5, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 34, 34, 34, 34, 34, 34, 34, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 34] 150 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/391 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@@H](O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1) `ZINC001454502051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454502051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001454502051 none COc1cccc([C@@H](O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 1, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 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, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 32, 32, 32, 32, 32, 14, 5, 14, 14, 5, 5, 5, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 32, 34, 34, 34, 32, 32, 32, 42, 5, 5, 5, 5, 5, 3, 3, 5, 5, 5, 5, 32] 150 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 129 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001454502051 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051 Building ZINC001454502051 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454502051 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 390) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1cccc([C@@H](O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1) `ZINC001454502051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454502051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001454502051 none COc1cccc([C@@H](O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 1, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 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, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 34, 34, 13, 5, 13, 13, 5, 5, 5, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 34, 34, 34, 34, 34, 34, 34, 39, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 34] 150 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 391) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1cccc([C@@H](O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1) `ZINC001454502051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454502051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001454502051 none COc1cccc([C@@H](O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 1, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 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, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 32, 32, 32, 32, 32, 14, 5, 14, 14, 5, 5, 5, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 32, 34, 34, 34, 32, 32, 32, 42, 5, 5, 5, 5, 5, 3, 3, 5, 5, 5, 5, 32] 150 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 129 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001454502051 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502051 Building ZINC001454502053 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454502053 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/392 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@H](O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1) `ZINC001454502053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454502053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001454502053 none COc1cccc([C@H](O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 1, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 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, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 36, 36, 12, 4, 12, 12, 4, 4, 4, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 36] 150 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/393 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc([C@H](O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1) `ZINC001454502053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454502053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001454502053 none COc1cccc([C@H](O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 1, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 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, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 12, 5, 12, 12, 5, 5, 5, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 29, 29, 29, 29, 29, 29, 29, 36, 5, 5, 5, 5, 5, 2, 2, 5, 5, 5, 5, 29] 150 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 109 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001454502053 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053 Building ZINC001454502053 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454502053 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 392) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1cccc([C@H](O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1) `ZINC001454502053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454502053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001454502053 none COc1cccc([C@H](O)C2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 1, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 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, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 36, 36, 12, 4, 12, 12, 4, 4, 4, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 36] 150 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 393) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1cccc([C@H](O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1) `ZINC001454502053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454502053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001454502053 none COc1cccc([C@H](O)C2CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 1, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 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, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 29, 29, 12, 5, 12, 12, 5, 5, 5, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 29, 29, 29, 29, 29, 29, 29, 36, 5, 5, 5, 5, 5, 2, 2, 5, 5, 5, 5, 29] 150 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 109 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001454502053 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454502053 Building ZINC001454937959 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454937959 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/394 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3ccn(Cc4ccc(CO)cc4)c3c2)cn1) `ZINC001454937959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454937959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001454937959 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3ccn(Cc4ccc(CO)cc4)c3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 5, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 34, 23, 23, 10, 10, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 10, 10, 10, 10, 23, 23, 23, 23, 34, 34, 102, 23, 23, 10, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/395 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3ccn(Cc4ccc(CO)cc4)c3c2)cn1) `ZINC001454937959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454937959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001454937959 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3ccn(Cc4ccc(CO)cc4)c3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 5, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22, 22, 22, 33, 22, 22, 10, 10, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 10, 10, 10, 10, 22, 22, 22, 22, 33, 33, 99, 22, 22, 10, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001454937959 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959 Building ZINC001454937959 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001454937959 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 394) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3ccn(Cc4ccc(CO)cc4)c3c2)cn1) `ZINC001454937959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001454937959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001454937959 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3ccn(Cc4ccc(CO)cc4)c3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 5, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 34, 23, 23, 10, 10, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 10, 10, 10, 10, 23, 23, 23, 23, 34, 34, 102, 23, 23, 10, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 395) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3ccn(Cc4ccc(CO)cc4)c3c2)cn1) `ZINC001454937959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001454937959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001454937959 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3ccn(Cc4ccc(CO)cc4)c3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 5, 12, 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, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 22, 22, 22, 22, 22, 33, 22, 22, 10, 10, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 10, 10, 10, 10, 22, 22, 22, 22, 33, 33, 99, 22, 22, 10, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001454937959 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001454937959 Building ZINC001455274922 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455274922 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/396 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOc2ccc(NC(=O)OC(C)(C)C)cc2C1) `ZINC001455274922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455274922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455274922 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOc2ccc(NC(=O)OC(C)(C)C)cc2C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 6, 6, 6, 24, 36, 36, 50, 50, 50, 50, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/397 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOc2ccc(NC(=O)OC(C)(C)C)cc2C1) `ZINC001455274922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455274922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455274922 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOc2ccc(NC(=O)OC(C)(C)C)cc2C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 6, 6, 6, 25, 36, 36, 50, 50, 50, 50, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455274922 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922 Building ZINC001455274922 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455274922 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 396) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOc2ccc(NC(=O)OC(C)(C)C)cc2C1) `ZINC001455274922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455274922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455274922 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOc2ccc(NC(=O)OC(C)(C)C)cc2C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 6, 6, 6, 24, 36, 36, 50, 50, 50, 50, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 397) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOc2ccc(NC(=O)OC(C)(C)C)cc2C1) `ZINC001455274922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455274922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001455274922 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOc2ccc(NC(=O)OC(C)(C)C)cc2C1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 6, 6, 6, 25, 36, 36, 50, 50, 50, 50, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455274922 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455274922 Building ZINC001455408924 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455408924 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/398 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)C2)CC1) `ZINC001455408924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455408924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001455408924 none CC(C)(C)OC(=O)N1CCC2(CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 24, 18, 24, 18, 18, 18, 18, 18, 2, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 38, 38, 38, 38, 38, 38, 38, 38, 38, 18, 18, 18, 18, 18, 18, 4, 4, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/399 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)C2)CC1) `ZINC001455408924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455408924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001455408924 none CC(C)(C)OC(=O)N1CCC2(CN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 22, 16, 22, 16, 16, 16, 16, 15, 2, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 15, 16, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 16, 16, 16, 16, 5, 5, 15, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455408924 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924 Building ZINC001455408924 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455408924 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 398) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)OC(=O)N1CCC2(CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)C2)CC1) `ZINC001455408924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455408924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001455408924 none CC(C)(C)OC(=O)N1CCC2(CN(C(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 24, 18, 24, 18, 18, 18, 18, 18, 2, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 38, 38, 38, 38, 38, 38, 38, 38, 38, 18, 18, 18, 18, 18, 18, 4, 4, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 399) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)OC(=O)N1CCC2(CN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)C2)CC1) `ZINC001455408924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455408924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001455408924 none CC(C)(C)OC(=O)N1CCC2(CN(C(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 22, 16, 22, 16, 16, 16, 16, 15, 2, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 15, 16, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36, 16, 16, 16, 16, 16, 16, 5, 5, 15, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455408924 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455408924 Building ZINC001455457603 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455457603 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/400 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/400' -> `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](C)c1ccncc1Br) `ZINC001455457603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455457603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001455457603 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccncc1Br 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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', '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, 1, 1, 1, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 11, 11, 7, 11, 11, 4, 4, 1, 1, 1, 1, 8, 8, 8, 14, 14, 14, 35, 35, 14, 35, 35, 35, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 8, 14, 14, 14, 35, 35, 35] 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]) total number of confs: 148 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/401 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/401' -> `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](C)c1ccncc1Br) `ZINC001455457603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455457603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001455457603 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccncc1Br 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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', '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, 1, 1, 1, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 11, 11, 7, 11, 11, 4, 4, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 34, 34, 13, 34, 34, 34, 4, 4, 4, 11, 11, 8, 11, 11, 4, 4, 4, 6, 13, 13, 13, 34, 34, 34] 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]) total number of confs: 152 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455457603 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603 Building ZINC001455457603 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455457603 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 400) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccncc1Br) `ZINC001455457603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455457603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001455457603 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccncc1Br 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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', '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, 1, 1, 1, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 11, 11, 7, 11, 11, 4, 4, 1, 1, 1, 1, 8, 8, 8, 14, 14, 14, 35, 35, 14, 35, 35, 35, 4, 4, 4, 11, 11, 4, 11, 11, 4, 4, 4, 8, 14, 14, 14, 35, 35, 35] 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]) total number of confs: 148 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 401) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccncc1Br) `ZINC001455457603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455457603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001455457603 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccncc1Br 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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', '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, 1, 1, 1, 8, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 11, 11, 7, 11, 11, 4, 4, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 34, 34, 13, 34, 34, 34, 4, 4, 4, 11, 11, 8, 11, 11, 4, 4, 4, 6, 13, 13, 13, 34, 34, 34] 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]) total number of confs: 152 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455457603 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455457603 Building ZINC001455715912 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455715912 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/402 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455715912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715912 none O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 16, 16, 32, 36, 36, 32, 36, 36, 16, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 2, 16, 16, 16, 16, 16, 16, 16, 16, 32, 32, 36, 36, 32, 36, 36, 16, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/403 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455715912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715912 none O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 16, 16, 32, 36, 36, 32, 36, 36, 16, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 2, 16, 16, 16, 16, 16, 16, 16, 16, 32, 32, 36, 36, 32, 36, 36, 16, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/404 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/404' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715912.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455715912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715912 none O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 40, 40, 34, 40, 40, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 3, 17, 17, 17, 17, 17, 17, 17, 17, 34, 34, 40, 40, 34, 40, 40, 17, 17, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/405 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/405' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715912.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455715912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715912 none O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 40, 40, 34, 40, 40, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 3, 17, 17, 17, 17, 17, 17, 17, 17, 34, 34, 40, 40, 34, 40, 40, 17, 17, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455715912 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 Building ZINC001455715912 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455715912 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 402) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455715912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715912 none O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 16, 16, 32, 36, 36, 32, 36, 36, 16, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 2, 16, 16, 16, 16, 16, 16, 16, 16, 32, 32, 36, 36, 32, 36, 36, 16, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 403) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455715912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715912 none O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 16, 16, 32, 36, 36, 32, 36, 36, 16, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 2, 16, 16, 16, 16, 16, 16, 16, 16, 32, 32, 36, 36, 32, 36, 36, 16, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 404) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715912.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455715912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715912 none O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 40, 40, 34, 40, 40, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 3, 17, 17, 17, 17, 17, 17, 17, 17, 34, 34, 40, 40, 34, 40, 40, 17, 17, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 405) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715912.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455715912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715912 none O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 40, 40, 34, 40, 40, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 3, 17, 17, 17, 17, 17, 17, 17, 17, 34, 34, 40, 40, 34, 40, 40, 17, 17, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455715912 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 Building ZINC001455715912 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455715912 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 402) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455715912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715912 none O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 16, 16, 32, 36, 36, 32, 36, 36, 16, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 2, 16, 16, 16, 16, 16, 16, 16, 16, 32, 32, 36, 36, 32, 36, 36, 16, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 403) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455715912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715912 none O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 16, 16, 32, 36, 36, 32, 36, 36, 16, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 2, 16, 16, 16, 16, 16, 16, 16, 16, 32, 32, 36, 36, 32, 36, 36, 16, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 404) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715912.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455715912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715912 none O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 40, 40, 34, 40, 40, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 3, 17, 17, 17, 17, 17, 17, 17, 17, 34, 34, 40, 40, 34, 40, 40, 17, 17, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 405) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715912.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455715912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715912 none O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 40, 40, 34, 40, 40, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 3, 17, 17, 17, 17, 17, 17, 17, 17, 34, 34, 40, 40, 34, 40, 40, 17, 17, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455715912 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 Building ZINC001455715912 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455715912 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 402) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455715912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715912 none O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 16, 16, 32, 36, 36, 32, 36, 36, 16, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 2, 16, 16, 16, 16, 16, 16, 16, 16, 32, 32, 36, 36, 32, 36, 36, 16, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 403) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455715912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715912 none O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 16, 16, 16, 16, 16, 16, 32, 36, 36, 32, 36, 36, 16, 16, 16, 1, 1, 1, 5, 5, 5, 5, 5, 2, 16, 16, 16, 16, 16, 16, 16, 16, 32, 32, 36, 36, 32, 36, 36, 16, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 404) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715912.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455715912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715912 none O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 40, 40, 34, 40, 40, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 3, 17, 17, 17, 17, 17, 17, 17, 17, 34, 34, 40, 40, 34, 40, 40, 17, 17, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 405) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715912.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455715912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715912 none O=C(N[C@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 17, 17, 17, 17, 17, 17, 34, 40, 40, 34, 40, 40, 17, 17, 17, 1, 1, 1, 5, 5, 5, 5, 5, 3, 17, 17, 17, 17, 17, 17, 17, 17, 34, 34, 40, 40, 34, 40, 40, 17, 17, 17, 17, 17, 17, 5, 5] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455715912 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715912 Building ZINC001455715914 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455715914 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/406 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455715914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715914 none O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 17, 19, 19, 19, 19, 19, 19, 19, 19, 36, 42, 42, 38, 42, 42, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 3, 19, 19, 19, 19, 19, 19, 19, 19, 36, 36, 42, 42, 37, 42, 42, 19, 19, 19, 19, 19, 19, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/407 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455715914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715914 none O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 17, 19, 19, 19, 19, 19, 19, 19, 19, 36, 42, 42, 38, 42, 42, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 3, 19, 19, 19, 19, 19, 19, 19, 19, 36, 36, 42, 42, 37, 42, 42, 19, 19, 19, 19, 19, 19, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/408 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/408' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715914.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455715914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715914 none O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 20, 20, 20, 20, 20, 20, 20, 20, 35, 42, 42, 40, 42, 42, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 2, 19, 20, 20, 20, 20, 20, 20, 20, 35, 35, 42, 42, 42, 42, 42, 20, 20, 20, 20, 20, 20, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/409 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/409' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715914.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455715914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715914 none O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 20, 20, 20, 20, 20, 20, 20, 20, 35, 42, 42, 40, 42, 42, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 2, 19, 20, 20, 20, 20, 20, 20, 20, 35, 35, 42, 42, 42, 42, 42, 20, 20, 20, 20, 20, 20, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455715914 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 Building ZINC001455715914 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455715914 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 406) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455715914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715914 none O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 17, 19, 19, 19, 19, 19, 19, 19, 19, 36, 42, 42, 38, 42, 42, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 3, 19, 19, 19, 19, 19, 19, 19, 19, 36, 36, 42, 42, 37, 42, 42, 19, 19, 19, 19, 19, 19, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 407) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455715914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715914 none O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 17, 19, 19, 19, 19, 19, 19, 19, 19, 36, 42, 42, 38, 42, 42, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 3, 19, 19, 19, 19, 19, 19, 19, 19, 36, 36, 42, 42, 37, 42, 42, 19, 19, 19, 19, 19, 19, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 408) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715914.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455715914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715914 none O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 20, 20, 20, 20, 20, 20, 20, 20, 35, 42, 42, 40, 42, 42, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 2, 19, 20, 20, 20, 20, 20, 20, 20, 35, 35, 42, 42, 42, 42, 42, 20, 20, 20, 20, 20, 20, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 409) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715914.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455715914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715914 none O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 20, 20, 20, 20, 20, 20, 20, 20, 35, 42, 42, 40, 42, 42, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 2, 19, 20, 20, 20, 20, 20, 20, 20, 35, 35, 42, 42, 42, 42, 42, 20, 20, 20, 20, 20, 20, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455715914 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 Building ZINC001455715914 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455715914 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 406) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455715914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715914 none O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 17, 19, 19, 19, 19, 19, 19, 19, 19, 36, 42, 42, 38, 42, 42, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 3, 19, 19, 19, 19, 19, 19, 19, 19, 36, 36, 42, 42, 37, 42, 42, 19, 19, 19, 19, 19, 19, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 407) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455715914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715914 none O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 17, 19, 19, 19, 19, 19, 19, 19, 19, 36, 42, 42, 38, 42, 42, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 3, 19, 19, 19, 19, 19, 19, 19, 19, 36, 36, 42, 42, 37, 42, 42, 19, 19, 19, 19, 19, 19, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 408) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715914.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455715914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715914 none O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 20, 20, 20, 20, 20, 20, 20, 20, 35, 42, 42, 40, 42, 42, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 2, 19, 20, 20, 20, 20, 20, 20, 20, 35, 35, 42, 42, 42, 42, 42, 20, 20, 20, 20, 20, 20, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 409) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715914.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455715914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715914 none O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 20, 20, 20, 20, 20, 20, 20, 20, 35, 42, 42, 40, 42, 42, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 2, 19, 20, 20, 20, 20, 20, 20, 20, 35, 35, 42, 42, 42, 42, 42, 20, 20, 20, 20, 20, 20, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455715914 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 Building ZINC001455715914 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001455715914 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 406) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455715914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715914 none O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 17, 19, 19, 19, 19, 19, 19, 19, 19, 36, 42, 42, 38, 42, 42, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 3, 19, 19, 19, 19, 19, 19, 19, 19, 36, 36, 42, 42, 37, 42, 42, 19, 19, 19, 19, 19, 19, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 407) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455715914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715914 none O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 17, 19, 19, 19, 19, 19, 19, 19, 19, 36, 42, 42, 38, 42, 42, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 3, 19, 19, 19, 19, 19, 19, 19, 19, 36, 36, 42, 42, 37, 42, 42, 19, 19, 19, 19, 19, 19, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 408) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715914.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001455715914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715914 none O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 20, 20, 20, 20, 20, 20, 20, 20, 35, 42, 42, 40, 42, 42, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 2, 19, 20, 20, 20, 20, 20, 20, 20, 35, 35, 42, 42, 42, 42, 42, 20, 20, 20, 20, 20, 20, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 409) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001455715914.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001455715914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001455715914 none O=C(N[C@@H]1CCOC2(CCN(Cc3ccccc3)CC2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 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', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', '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', '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, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 1, 1, 1, 1, 16, 14, 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: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 20, 20, 20, 20, 20, 20, 20, 20, 35, 42, 42, 40, 42, 42, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 2, 19, 20, 20, 20, 20, 20, 20, 20, 35, 35, 42, 42, 42, 42, 42, 20, 20, 20, 20, 20, 20, 6, 6] 50 rigid atoms, others: [24, 1, 22, 23] set([0, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455715914 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455715914 Building ZINC001455784827 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455784827 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/410 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccn(c2ccc(Br)cc2)n1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001455784827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455784827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001455784827 none O=C(NCc1ccn(c2ccc(Br)cc2)n1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 20, 20, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/411 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccn(c2ccc(Br)cc2)n1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001455784827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455784827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001455784827 none O=C(NCc1ccn(c2ccc(Br)cc2)n1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 20, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 20, 20, 33, 33, 33, 33, 33, 33, 4, 4, 4, 4] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455784827 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827 Building ZINC001455784827 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455784827 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 410) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCc1ccn(c2ccc(Br)cc2)n1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001455784827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455784827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001455784827 none O=C(NCc1ccn(c2ccc(Br)cc2)n1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 20, 20, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 411) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCc1ccn(c2ccc(Br)cc2)n1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001455784827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455784827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001455784827 none O=C(NCc1ccn(c2ccc(Br)cc2)n1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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: [11, 1, 8, 5, 1, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 8, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 20, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 20, 20, 33, 33, 33, 33, 33, 33, 4, 4, 4, 4] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455784827 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455784827 Building ZINC001455952260 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455952260 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/412 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001455952260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455952260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001455952260 none CC(C)(C)OC(=O)N1CCC[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 28, 42, 28, 28, 28, 28, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 28, 15, 15, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/413 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@]1(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001455952260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455952260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001455952260 none CC(C)(C)OC(=O)N1CCC[C@@]1(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 29, 41, 29, 29, 29, 29, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 16, 16, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455952260 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260 Building ZINC001455952260 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455952260 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 412) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCC[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001455952260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455952260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001455952260 none CC(C)(C)OC(=O)N1CCC[C@@]1(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 28, 42, 28, 28, 28, 28, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 28, 15, 15, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 413) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCC[C@@]1(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001455952260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455952260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001455952260 none CC(C)(C)OC(=O)N1CCC[C@@]1(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 29, 41, 29, 29, 29, 29, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 16, 16, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455952260 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952260 Building ZINC001455952267 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455952267 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/414 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@]1(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001455952267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455952267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001455952267 none CC(C)(C)OC(=O)N1CCC[C@]1(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 30, 43, 30, 30, 30, 30, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 15, 15, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/415 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@]1(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001455952267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455952267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001455952267 none CC(C)(C)OC(=O)N1CCC[C@]1(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 29, 42, 29, 29, 29, 29, 21, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 15, 15, 5, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455952267 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267 Building ZINC001455952267 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455952267 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 414) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCC[C@]1(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001455952267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455952267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001455952267 none CC(C)(C)OC(=O)N1CCC[C@]1(CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 30, 43, 30, 30, 30, 30, 18, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 15, 15, 4, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 415) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCC[C@]1(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F) `ZINC001455952267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455952267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001455952267 none CC(C)(C)OC(=O)N1CCC[C@]1(CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 29, 42, 29, 29, 29, 29, 21, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 29, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 15, 15, 5, 3, 3, 3, 3] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455952267 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455952267 Building ZINC001455983651 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455983651 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/416 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)n(c2ncccn2)n1) `ZINC001455983651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455983651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001455983651 none CC(C)(C)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)n(c2ncccn2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 1, 8, 1, 1, 1, 8, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 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: [33, 19, 33, 33, 19, 19, 11, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 11, 9, 9, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/417 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)n(c2ncccn2)n1) `ZINC001455983651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455983651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001455983651 none CC(C)(C)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)n(c2ncccn2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 1, 8, 1, 1, 1, 8, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 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: [33, 18, 33, 33, 18, 18, 11, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 18, 11, 8, 8, 18, 18, 18] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455983651 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651 Building ZINC001455983651 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001455983651 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 416) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)n(c2ncccn2)n1) `ZINC001455983651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001455983651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001455983651 none CC(C)(C)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)n(c2ncccn2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 1, 8, 1, 1, 1, 8, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 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: [33, 19, 33, 33, 19, 19, 11, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 11, 9, 9, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 417) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)n(c2ncccn2)n1) `ZINC001455983651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001455983651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001455983651 none CC(C)(C)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)n(c2ncccn2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 8, 1, 8, 1, 1, 1, 8, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 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: [33, 18, 33, 33, 18, 18, 11, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 18, 11, 8, 8, 18, 18, 18] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001455983651 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001455983651 Building ZINC001456087863 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456087863 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/418 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C2CC2)nc1C) `ZINC001456087863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456087863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001456087863 none CCOC(=O)c1sc(N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C2CC2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 8, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 12, 34, 12, 12, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 5, 7, 7, 12, 12, 12, 37, 37, 37, 37, 37, 4, 4, 7, 7, 7, 7, 7, 12, 12, 12] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/419 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc(N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C2CC2)nc1C) `ZINC001456087863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456087863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001456087863 none CCOC(=O)c1sc(N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C2CC2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 8, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 13, 34, 13, 13, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 6, 8, 8, 13, 13, 13, 37, 37, 37, 37, 37, 4, 4, 8, 8, 8, 8, 8, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456087863 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863 Building ZINC001456087863 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456087863 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 418) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1sc(N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C2CC2)nc1C) `ZINC001456087863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456087863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001456087863 none CCOC(=O)c1sc(N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C2CC2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 8, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 12, 34, 12, 12, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 5, 7, 7, 12, 12, 12, 37, 37, 37, 37, 37, 4, 4, 7, 7, 7, 7, 7, 12, 12, 12] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 419) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1sc(N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C2CC2)nc1C) `ZINC001456087863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456087863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC001456087863 none CCOC(=O)c1sc(N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C2CC2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 8, 1, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 13, 34, 13, 13, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 6, 8, 8, 13, 13, 13, 37, 37, 37, 37, 37, 4, 4, 8, 8, 8, 8, 8, 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456087863 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456087863 Building ZINC001456105863 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456105863 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/420 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCN(c2ccccc2Cl)C1=O) `ZINC001456105863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456105863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001456105863 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCN(c2ccccc2Cl)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 9, 11, 11, 11, 11, 11, 31, 31, 11, 31, 31, 31, 11, 11, 6, 6, 6, 3, 3, 11, 11, 11, 11, 31, 31, 28, 31] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/421 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCN(c2ccccc2Cl)C1=O) `ZINC001456105863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456105863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001456105863 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCN(c2ccccc2Cl)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 12, 12, 12, 12, 12, 32, 32, 12, 32, 32, 32, 12, 12, 3, 3, 3, 3, 3, 12, 12, 12, 12, 32, 32, 31, 32] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456105863 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863 Building ZINC001456105863 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456105863 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 420) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCN(c2ccccc2Cl)C1=O) `ZINC001456105863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456105863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001456105863 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCN(c2ccccc2Cl)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 9, 11, 11, 11, 11, 11, 31, 31, 11, 31, 31, 31, 11, 11, 6, 6, 6, 3, 3, 11, 11, 11, 11, 31, 31, 28, 31] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 421) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCN(c2ccccc2Cl)C1=O) `ZINC001456105863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456105863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001456105863 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@@H]1CCN(c2ccccc2Cl)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 12, 12, 12, 12, 12, 32, 32, 12, 32, 32, 32, 12, 12, 3, 3, 3, 3, 3, 12, 12, 12, 12, 32, 32, 31, 32] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456105863 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105863 Building ZINC001456105870 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456105870 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/422 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCN(c2ccccc2Cl)C1=O) `ZINC001456105870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456105870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001456105870 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCN(c2ccccc2Cl)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 11, 11, 11, 11, 11, 31, 31, 18, 31, 31, 31, 11, 11, 3, 3, 3, 3, 3, 11, 11, 11, 11, 31, 31, 31, 31] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/423 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCN(c2ccccc2Cl)C1=O) `ZINC001456105870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456105870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001456105870 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCN(c2ccccc2Cl)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 9, 11, 11, 11, 11, 11, 32, 32, 32, 32, 32, 32, 11, 11, 6, 6, 6, 3, 3, 11, 11, 11, 11, 32, 32, 32, 32] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456105870 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870 Building ZINC001456105870 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456105870 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 422) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCN(c2ccccc2Cl)C1=O) `ZINC001456105870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456105870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001456105870 none CN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCN(c2ccccc2Cl)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 11, 11, 11, 11, 11, 31, 31, 18, 31, 31, 31, 11, 11, 3, 3, 3, 3, 3, 11, 11, 11, 11, 31, 31, 31, 31] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 423) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCN(c2ccccc2Cl)C1=O) `ZINC001456105870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456105870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001456105870 none CN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)[C@H]1CCN(c2ccccc2Cl)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 16, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 9, 11, 11, 11, 11, 11, 32, 32, 32, 32, 32, 32, 11, 11, 6, 6, 6, 3, 3, 11, 11, 11, 11, 32, 32, 32, 32] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456105870 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456105870 Building ZINC001456112382 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456112382 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/424 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/424' -> `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(c2ccccc2)c1C)C1CCCCCC1) `ZINC001456112382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456112382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001456112382 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C1CCCCCC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 24, 29, 10, 24, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 38, 42, 42, 42, 42, 42, 42, 29, 29, 29, 10, 10, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/425 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/425' -> `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(c2ccccc2)c1C)C1CCCCCC1) `ZINC001456112382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456112382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001456112382 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C1CCCCCC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 25, 8, 24, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 37, 42, 42, 42, 42, 42, 42, 25, 25, 25, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456112382 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382 Building ZINC001456112382 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456112382 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 424) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C1CCCCCC1) `ZINC001456112382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456112382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001456112382 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C1CCCCCC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 24, 29, 10, 24, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 38, 42, 42, 42, 42, 42, 42, 29, 29, 29, 10, 10, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 425) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C1CCCCCC1) `ZINC001456112382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456112382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001456112382 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C1CCCCCC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 25, 8, 24, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 37, 42, 42, 42, 42, 42, 42, 25, 25, 25, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456112382 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112382 Building ZINC001456112384 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456112384 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/426 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/426' -> `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(c2ccccc2)c1C)C1CCCCCC1) `ZINC001456112384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456112384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001456112384 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C1CCCCCC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 27, 8, 23, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 29, 39, 39, 39, 39, 39, 39, 27, 27, 27, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/427 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/427' -> `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(c2ccccc2)c1C)C1CCCCCC1) `ZINC001456112384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456112384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001456112384 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C1CCCCCC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 27, 10, 23, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 26, 37, 37, 37, 37, 37, 37, 27, 27, 27, 10, 10, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456112384 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384 Building ZINC001456112384 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456112384 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 426) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C1CCCCCC1) `ZINC001456112384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456112384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001456112384 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C1CCCCCC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 27, 8, 23, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 29, 39, 39, 39, 39, 39, 39, 27, 27, 27, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 427) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C1CCCCCC1) `ZINC001456112384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456112384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001456112384 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C1CCCCCC1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 27, 10, 23, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 26, 37, 37, 37, 37, 37, 37, 27, 27, 27, 10, 10, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 162 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456112384 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456112384 Building ZINC001456130137 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456130137 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/428 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001456130137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456130137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456130137 none CC(C)(C)OC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 48, 45, 48, 31, 31, 31, 31, 31, 15, 31, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 45, 31, 31, 31, 31, 11, 11, 2, 3, 3, 31, 31] 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, 43, 44, 45, 46, 47]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/429 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001456130137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456130137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456130137 none CC(C)(C)OC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 43, 47, 30, 30, 30, 30, 30, 15, 30, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 30, 48, 48, 48, 48, 48, 48, 48, 48, 48, 43, 30, 30, 30, 30, 12, 12, 2, 4, 4, 30, 30] 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, 43, 44, 45, 46, 47]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456130137 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137 Building ZINC001456130137 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456130137 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 428) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001456130137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456130137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456130137 none CC(C)(C)OC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 48, 45, 48, 31, 31, 31, 31, 31, 15, 31, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 31, 49, 49, 49, 49, 49, 49, 49, 49, 49, 45, 31, 31, 31, 31, 11, 11, 2, 3, 3, 31, 31] 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, 43, 44, 45, 46, 47]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 429) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001456130137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456130137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456130137 none CC(C)(C)OC(=O)N[C@@H]1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 43, 47, 30, 30, 30, 30, 30, 15, 30, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 30, 48, 48, 48, 48, 48, 48, 48, 48, 48, 43, 30, 30, 30, 30, 12, 12, 2, 4, 4, 30, 30] 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, 43, 44, 45, 46, 47]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456130137 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456130137 Building ZINC001456137989 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456137989 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/430 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@](CNC(=O)OC(C)(C)C)(c2ccccc2)C1) `ZINC001456137989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456137989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001456137989 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@](CNC(=O)OC(C)(C)C)(c2ccccc2)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.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.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', '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, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 9, 25, 41, 50, 50, 50, 50, 50, 50, 9, 16, 16, 9, 16, 16, 9, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 25, 25, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 9, 16, 16, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/431 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@](CNC(=O)OC(C)(C)C)(c2ccccc2)C1) `ZINC001456137989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456137989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001456137989 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@](CNC(=O)OC(C)(C)C)(c2ccccc2)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.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.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', '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, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 9, 22, 38, 50, 50, 50, 50, 50, 50, 9, 15, 15, 9, 15, 15, 9, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 22, 22, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 9, 15, 15, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456137989 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989 Building ZINC001456137989 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456137989 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 430) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@](CNC(=O)OC(C)(C)C)(c2ccccc2)C1) `ZINC001456137989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456137989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001456137989 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@](CNC(=O)OC(C)(C)C)(c2ccccc2)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.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.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', '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, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 9, 25, 41, 50, 50, 50, 50, 50, 50, 9, 16, 16, 9, 16, 16, 9, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 25, 25, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 9, 16, 16, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 431) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@](CNC(=O)OC(C)(C)C)(c2ccccc2)C1) `ZINC001456137989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456137989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001456137989 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@](CNC(=O)OC(C)(C)C)(c2ccccc2)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.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.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', '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, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 9, 22, 38, 50, 50, 50, 50, 50, 50, 9, 15, 15, 9, 15, 15, 9, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 22, 22, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 9, 15, 15, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456137989 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456137989 Building ZINC001456324941 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456324941 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/432 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(S(=O)(=O)C[C@@H]2CCCO2)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456324941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456324941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001456324941 none O=C(Nc1ccc(S(=O)(=O)C[C@@H]2CCCO2)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 14, 11, 11, 5, 5, 7, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 3, 7, 7, 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] 0 hydrogens need 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, 7, 7, 4, 7, 14, 14, 14, 39, 46, 46, 46, 46, 46, 7, 7, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 7, 7, 35, 35, 46, 46, 46, 46, 46, 46, 7, 7, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/433 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/433' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(S(=O)(=O)C[C@@H]2CCCO2)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456324941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456324941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001456324941 none O=C(Nc1ccc(S(=O)(=O)C[C@@H]2CCCO2)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 14, 11, 11, 5, 5, 7, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 3, 7, 7, 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] 0 hydrogens need 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, 8, 8, 2, 8, 13, 13, 13, 35, 43, 43, 43, 43, 43, 8, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 8, 8, 30, 30, 43, 43, 43, 43, 43, 43, 8, 8, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456324941 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941 Building ZINC001456324941 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456324941 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 432) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(S(=O)(=O)C[C@@H]2CCCO2)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456324941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456324941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001456324941 none O=C(Nc1ccc(S(=O)(=O)C[C@@H]2CCCO2)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 14, 11, 11, 5, 5, 7, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 3, 7, 7, 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] 0 hydrogens need 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, 7, 7, 4, 7, 14, 14, 14, 39, 46, 46, 46, 46, 46, 7, 7, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 7, 7, 35, 35, 46, 46, 46, 46, 46, 46, 7, 7, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 433) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(S(=O)(=O)C[C@@H]2CCCO2)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456324941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456324941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001456324941 none O=C(Nc1ccc(S(=O)(=O)C[C@@H]2CCCO2)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 14, 11, 11, 5, 5, 7, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 3, 7, 7, 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] 0 hydrogens need 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, 8, 8, 2, 8, 13, 13, 13, 35, 43, 43, 43, 43, 43, 8, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 8, 8, 30, 30, 43, 43, 43, 43, 43, 43, 8, 8, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456324941 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324941 Building ZINC001456324945 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456324945 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/434 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(S(=O)(=O)C[C@H]2CCCO2)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456324945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456324945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001456324945 none O=C(Nc1ccc(S(=O)(=O)C[C@H]2CCCO2)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 14, 11, 11, 5, 5, 7, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 3, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 5, 8, 13, 13, 13, 38, 45, 45, 45, 45, 45, 8, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 8, 8, 31, 31, 45, 45, 45, 45, 45, 45, 8, 8, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/435 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(S(=O)(=O)C[C@H]2CCCO2)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456324945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456324945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001456324945 none O=C(Nc1ccc(S(=O)(=O)C[C@H]2CCCO2)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 14, 11, 11, 5, 5, 7, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 3, 7, 7, 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] 0 hydrogens need 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, 7, 7, 4, 7, 13, 13, 13, 38, 45, 45, 45, 45, 45, 7, 7, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 7, 7, 33, 33, 45, 45, 45, 45, 45, 45, 7, 7, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456324945 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945 Building ZINC001456324945 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456324945 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 434) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(S(=O)(=O)C[C@H]2CCCO2)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456324945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456324945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001456324945 none O=C(Nc1ccc(S(=O)(=O)C[C@H]2CCCO2)cc1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 14, 11, 11, 5, 5, 7, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 3, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 5, 8, 13, 13, 13, 38, 45, 45, 45, 45, 45, 8, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 8, 8, 31, 31, 45, 45, 45, 45, 45, 45, 8, 8, 3, 1, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 435) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(S(=O)(=O)C[C@H]2CCCO2)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456324945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456324945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001456324945 none O=C(Nc1ccc(S(=O)(=O)C[C@H]2CCCO2)cc1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 1, 14, 11, 11, 5, 5, 7, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 3, 7, 7, 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] 0 hydrogens need 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, 7, 7, 4, 7, 13, 13, 13, 38, 45, 45, 45, 45, 45, 7, 7, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 7, 7, 33, 33, 45, 45, 45, 45, 45, 45, 7, 7, 3, 3, 3] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456324945 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456324945 Building ZINC001456333678 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456333678 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/436 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/436' -> `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](C)c2ccc(Br)cc2)CC1) `ZINC001456333678.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456333678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001456333678 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2ccc(Br)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.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, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 1, 1, 1, 17, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 6, 21, 21, 21, 21, 46, 46, 46, 47, 47, 47, 47, 47, 47, 21, 21, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 46, 46, 46, 47, 47, 47, 47, 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, 48]) total number of confs: 145 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/437 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/437' -> `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](C)c2ccc(Br)cc2)CC1) `ZINC001456333678.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456333678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001456333678 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2ccc(Br)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.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, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 1, 1, 1, 17, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 6, 18, 18, 18, 18, 47, 47, 47, 48, 48, 48, 48, 48, 48, 18, 18, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 47, 47, 47, 48, 48, 48, 48, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 159 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456333678 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678 Building ZINC001456333678 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456333678 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 436) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2ccc(Br)cc2)CC1) `ZINC001456333678.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456333678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001456333678 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2ccc(Br)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.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, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 1, 1, 1, 17, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 6, 21, 21, 21, 21, 46, 46, 46, 47, 47, 47, 47, 47, 47, 21, 21, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 46, 46, 46, 47, 47, 47, 47, 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, 48]) total number of confs: 145 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 437) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2ccc(Br)cc2)CC1) `ZINC001456333678.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456333678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001456333678 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2ccc(Br)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.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, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 1, 1, 1, 17, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 6, 18, 18, 18, 18, 47, 47, 47, 48, 48, 48, 48, 48, 48, 18, 18, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 47, 47, 47, 48, 48, 48, 48, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 159 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456333678 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333678 Building ZINC001456333681 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456333681 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/438 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/438' -> `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](C)c2ccc(Br)cc2)CC1) `ZINC001456333681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456333681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001456333681 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H](C)c2ccc(Br)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.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, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 1, 1, 1, 17, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 6, 19, 19, 19, 19, 46, 46, 46, 46, 46, 46, 46, 46, 46, 19, 19, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 46, 46, 46, 46, 46, 46, 46, 19, 19, 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]) total number of confs: 156 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/439 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/439' -> `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](C)c2ccc(Br)cc2)CC1) `ZINC001456333681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456333681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001456333681 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H](C)c2ccc(Br)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.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, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 1, 1, 1, 17, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 20, 20, 20, 20, 48, 48, 48, 49, 49, 49, 49, 49, 49, 20, 20, 3, 3, 3, 3, 3, 3, 20, 20, 20, 20, 48, 48, 48, 49, 49, 49, 49, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 157 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456333681 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681 Building ZINC001456333681 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456333681 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 438) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H](C)c2ccc(Br)cc2)CC1) `ZINC001456333681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456333681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001456333681 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H](C)c2ccc(Br)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.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, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 1, 1, 1, 17, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 6, 19, 19, 19, 19, 46, 46, 46, 46, 46, 46, 46, 46, 46, 19, 19, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 46, 46, 46, 46, 46, 46, 46, 19, 19, 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]) total number of confs: 156 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 439) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H](C)c2ccc(Br)cc2)CC1) `ZINC001456333681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456333681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001456333681 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H](C)c2ccc(Br)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.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, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 1, 1, 1, 17, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 20, 20, 20, 20, 48, 48, 48, 49, 49, 49, 49, 49, 49, 20, 20, 3, 3, 3, 3, 3, 3, 20, 20, 20, 20, 48, 48, 48, 49, 49, 49, 49, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 157 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456333681 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456333681 Building ZINC001456370961 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456370961 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/440 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(CNC(=O)OC(C)(C)C)[nH]c2c1) `ZINC001456370961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456370961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001456370961 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(CNC(=O)OC(C)(C)C)[nH]c2c1 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', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 6, 1, 1, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 38, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/441 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(CNC(=O)OC(C)(C)C)[nH]c2c1) `ZINC001456370961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456370961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001456370961 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(CNC(=O)OC(C)(C)C)[nH]c2c1 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', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 6, 1, 1, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 36, 49, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 36, 36, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456370961 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961 Building ZINC001456370961 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456370961 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 440) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(CNC(=O)OC(C)(C)C)[nH]c2c1) `ZINC001456370961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456370961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001456370961 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nc(CNC(=O)OC(C)(C)C)[nH]c2c1 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', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 6, 1, 1, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 38, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 441) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(CNC(=O)OC(C)(C)C)[nH]c2c1) `ZINC001456370961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456370961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001456370961 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1ccc2nc(CNC(=O)OC(C)(C)C)[nH]c2c1 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', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 6, 1, 1, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 36, 49, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 3, 12, 12, 36, 36, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456370961 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456370961 Building ZINC001456417219 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456417219 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/442 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ccccc1O2) `ZINC001456417219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456417219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001456417219 none CC(C)(C)OC(=O)N1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 25, 13, 25, 13, 13, 13, 13, 13, 13, 13, 9, 2, 13, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [51, 54, 57, 50, 17, 18, 19, 20, 21, 22, 55, 56, 52, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 59, 60, 61, 62, 63, 64]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/443 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ccccc1O2) `ZINC001456417219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456417219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001456417219 none CC(C)(C)OC(=O)N1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 25, 14, 25, 14, 14, 14, 14, 14, 14, 14, 10, 3, 14, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [51, 54, 57, 50, 17, 18, 19, 20, 21, 22, 55, 56, 52, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 59, 60, 61, 62, 63, 64]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456417219 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219 Building ZINC001456417219 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456417219 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 442) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)OC(=O)N1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ccccc1O2) `ZINC001456417219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456417219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001456417219 none CC(C)(C)OC(=O)N1CCC2(CC1)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)Cc1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 25, 13, 25, 13, 13, 13, 13, 13, 13, 13, 9, 2, 13, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [51, 54, 57, 50, 17, 18, 19, 20, 21, 22, 55, 56, 52, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 59, 60, 61, 62, 63, 64]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 443) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)OC(=O)N1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ccccc1O2) `ZINC001456417219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456417219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001456417219 none CC(C)(C)OC(=O)N1CCC2(CC1)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)Cc1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 25, 14, 25, 14, 14, 14, 14, 14, 14, 14, 10, 3, 14, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [51, 54, 57, 50, 17, 18, 19, 20, 21, 22, 55, 56, 52, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 59, 60, 61, 62, 63, 64]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456417219 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456417219 Building ZINC001456523015 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456523015 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/444 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1csc(CC2(O)C[C@H]3CC[C@@H](C2)N3C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n1) `ZINC001456523015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456523015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001456523015 none CC(C)(C)c1csc(CC2(O)C[C@H]3CC[C@@H](C2)N3C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 5, 12, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 15, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2] 150 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 119 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/445 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)c1csc(CC2(O)C[C@H]3CC[C@@H](C2)N3C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n1) `ZINC001456523015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456523015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001456523015 none CC(C)(C)c1csc(CC2(O)C[C@H]3CC[C@@H](C2)N3C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 5, 12, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 15, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2] 150 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 122 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456523015 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015 Building ZINC001456523015 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456523015 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 444) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)c1csc(CC2(O)C[C@H]3CC[C@@H](C2)N3C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n1) `ZINC001456523015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456523015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001456523015 none CC(C)(C)c1csc(CC2(O)C[C@H]3CC[C@@H](C2)N3C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 5, 12, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 15, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2] 150 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 119 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 445) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)c1csc(CC2(O)C[C@H]3CC[C@@H](C2)N3C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n1) `ZINC001456523015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456523015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001456523015 none CC(C)(C)c1csc(CC2(O)C[C@H]3CC[C@@H](C2)N3C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 14, 1, 5, 5, 12, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 15, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2] 150 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 122 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456523015 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456523015 Building ZINC001456613481 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456613481 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/446 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@](O)(c2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001456613481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456613481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001456613481 none O=C(N1CCC[C@@](O)(c2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 2, 17, 22, 22, 22, 22, 22, 22, 35, 35, 27, 27, 35, 35, 22, 1, 1, 1, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 66, 35, 35, 35, 35, 22, 22, 8, 8] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 158 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/447 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@](O)(c2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001456613481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456613481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001456613481 none O=C(N1CCC[C@@](O)(c2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens 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, 2, 15, 21, 21, 21, 21, 21, 21, 33, 33, 28, 28, 33, 33, 21, 1, 1, 1, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 63, 33, 33, 33, 33, 21, 21, 6, 6] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 148 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456613481 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481 Building ZINC001456613481 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456613481 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 446) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCC[C@@](O)(c2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001456613481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456613481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001456613481 none O=C(N1CCC[C@@](O)(c2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 2, 17, 22, 22, 22, 22, 22, 22, 35, 35, 27, 27, 35, 35, 22, 1, 1, 1, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 66, 35, 35, 35, 35, 22, 22, 8, 8] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 158 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 447) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCC[C@@](O)(c2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001456613481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456613481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001456613481 none O=C(N1CCC[C@@](O)(c2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens 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, 2, 15, 21, 21, 21, 21, 21, 21, 33, 33, 28, 28, 33, 33, 21, 1, 1, 1, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 63, 33, 33, 33, 33, 21, 21, 6, 6] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 148 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456613481 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613481 Building ZINC001456613482 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456613482 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/448 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@](O)(c2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001456613482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456613482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001456613482 none O=C(N1CCC[C@](O)(c2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 17, 25, 25, 25, 25, 25, 25, 34, 34, 32, 34, 34, 34, 25, 1, 1, 1, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 75, 34, 34, 34, 34, 25, 25, 6, 6] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 152 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/449 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@](O)(c2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001456613482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456613482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001456613482 none O=C(N1CCC[C@](O)(c2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens 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, 16, 22, 22, 22, 22, 22, 22, 36, 36, 28, 28, 36, 36, 22, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 66, 36, 36, 36, 36, 22, 22, 7, 7] 150 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]) total number of confs: 158 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456613482 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482 Building ZINC001456613482 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456613482 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 448) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCC[C@](O)(c2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001456613482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456613482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001456613482 none O=C(N1CCC[C@](O)(c2ccc(Br)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 17, 25, 25, 25, 25, 25, 25, 34, 34, 32, 34, 34, 34, 25, 1, 1, 1, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 75, 34, 34, 34, 34, 25, 25, 6, 6] 150 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 152 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 449) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCC[C@](O)(c2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001456613482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456613482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001456613482 none O=C(N1CCC[C@](O)(c2ccc(Br)cc2)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens 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, 16, 22, 22, 22, 22, 22, 22, 36, 36, 28, 28, 36, 36, 22, 1, 1, 1, 7, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 66, 36, 36, 36, 36, 22, 22, 7, 7] 150 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]) total number of confs: 158 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456613482 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456613482 Building ZINC001456920692 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001456920692 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/450 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc([N@]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001456920692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456920692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456920692 none CN(C)c1ccc([N@]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 25, 37, 23, 30, 30, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 30, 30, 37, 37, 37, 37, 37, 37, 30, 30, 15, 15, 15, 15, 2, 7, 7, 15, 15, 15, 15, 30, 30] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/451 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc([N@]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001456920692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456920692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456920692 none CN(C)c1ccc([N@]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 36, 16, 31, 31, 16, 16, 16, 16, 5, 16, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 16, 16, 31, 31, 36, 36, 36, 36, 36, 36, 31, 31, 16, 16, 16, 16, 3, 7, 7, 16, 16, 16, 16, 31, 31] 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/452 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/452' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc([N@]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001456920692.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001456920692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456920692 none CN(C)c1ccc([N@]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 36, 25, 30, 30, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 30, 30, 36, 36, 36, 36, 36, 36, 30, 30, 15, 15, 15, 15, 2, 7, 7, 15, 15, 15, 15, 30, 30] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/453 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/453' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc([N@]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001456920692.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001456920692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456920692 none CN(C)c1ccc([N@]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 36, 25, 30, 30, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 30, 30, 36, 36, 36, 36, 36, 36, 30, 30, 15, 15, 15, 15, 2, 7, 7, 15, 15, 15, 15, 30, 30] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456920692 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 Building ZINC001456920692 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001456920692 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 450) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C)c1ccc([N@]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001456920692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456920692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456920692 none CN(C)c1ccc([N@]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 25, 37, 23, 30, 30, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 30, 30, 37, 37, 37, 37, 37, 37, 30, 30, 15, 15, 15, 15, 2, 7, 7, 15, 15, 15, 15, 30, 30] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 451) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C)c1ccc([N@]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001456920692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456920692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456920692 none CN(C)c1ccc([N@]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 36, 16, 31, 31, 16, 16, 16, 16, 5, 16, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 16, 16, 31, 31, 36, 36, 36, 36, 36, 36, 31, 31, 16, 16, 16, 16, 3, 7, 7, 16, 16, 16, 16, 31, 31] 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 452) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc([N@]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001456920692.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001456920692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456920692 none CN(C)c1ccc([N@]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 36, 25, 30, 30, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 30, 30, 36, 36, 36, 36, 36, 36, 30, 30, 15, 15, 15, 15, 2, 7, 7, 15, 15, 15, 15, 30, 30] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 453) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc([N@]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001456920692.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001456920692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456920692 none CN(C)c1ccc([N@]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 36, 25, 30, 30, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 30, 30, 36, 36, 36, 36, 36, 36, 30, 30, 15, 15, 15, 15, 2, 7, 7, 15, 15, 15, 15, 30, 30] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456920692 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 Building ZINC001456920692 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001456920692 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 450) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C)c1ccc([N@]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001456920692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456920692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456920692 none CN(C)c1ccc([N@]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 25, 37, 23, 30, 30, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 30, 30, 37, 37, 37, 37, 37, 37, 30, 30, 15, 15, 15, 15, 2, 7, 7, 15, 15, 15, 15, 30, 30] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 451) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C)c1ccc([N@]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001456920692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456920692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456920692 none CN(C)c1ccc([N@]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 36, 16, 31, 31, 16, 16, 16, 16, 5, 16, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 16, 16, 31, 31, 36, 36, 36, 36, 36, 36, 31, 31, 16, 16, 16, 16, 3, 7, 7, 16, 16, 16, 16, 31, 31] 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 452) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc([N@]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001456920692.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001456920692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456920692 none CN(C)c1ccc([N@]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 36, 25, 30, 30, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 30, 30, 36, 36, 36, 36, 36, 36, 30, 30, 15, 15, 15, 15, 2, 7, 7, 15, 15, 15, 15, 30, 30] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 453) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc([N@]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001456920692.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001456920692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456920692 none CN(C)c1ccc([N@]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 36, 25, 30, 30, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 30, 30, 36, 36, 36, 36, 36, 36, 30, 30, 15, 15, 15, 15, 2, 7, 7, 15, 15, 15, 15, 30, 30] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456920692 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 Building ZINC001456920692 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001456920692 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 450) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C)c1ccc([N@]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001456920692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456920692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456920692 none CN(C)c1ccc([N@]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 25, 37, 23, 30, 30, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 30, 30, 37, 37, 37, 37, 37, 37, 30, 30, 15, 15, 15, 15, 2, 7, 7, 15, 15, 15, 15, 30, 30] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 451) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C)c1ccc([N@]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001456920692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456920692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456920692 none CN(C)c1ccc([N@]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 36, 16, 31, 31, 16, 16, 16, 16, 5, 16, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 16, 16, 31, 31, 36, 36, 36, 36, 36, 36, 31, 31, 16, 16, 16, 16, 3, 7, 7, 16, 16, 16, 16, 31, 31] 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 452) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc([N@]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001456920692.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001456920692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456920692 none CN(C)c1ccc([N@]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 36, 25, 30, 30, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 30, 30, 36, 36, 36, 36, 36, 36, 30, 30, 15, 15, 15, 15, 2, 7, 7, 15, 15, 15, 15, 30, 30] 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 453) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1ccc([N@]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1) `ZINC001456920692.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001456920692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001456920692 none CN(C)c1ccc([N@]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc(Br)s3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.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, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 36, 25, 30, 30, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 15, 15, 30, 30, 36, 36, 36, 36, 36, 36, 30, 30, 15, 15, 15, 15, 2, 7, 7, 15, 15, 15, 15, 30, 30] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456920692 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456920692 Building ZINC001456984388 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456984388 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/454 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456984388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456984388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001456984388 none COCC[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 6, 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, 7, 7, 7] 0 hydrogens 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, 17, 12, 8, 8, 8, 8, 8, 8, 18, 18, 33, 33, 33, 33, 8, 8, 6, 1, 6, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 22, 22, 22, 17, 17, 12, 12, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 8, 8, 8, 8, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/455 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456984388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456984388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001456984388 none COCC[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 6, 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, 7, 7, 7] 0 hydrogens 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, 9, 5, 5, 5, 5, 5, 5, 10, 10, 27, 27, 27, 27, 5, 5, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 22, 22, 22, 15, 15, 9, 9, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456984388 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388 Building ZINC001456984388 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456984388 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 454) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COCC[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456984388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456984388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001456984388 none COCC[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 6, 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, 7, 7, 7] 0 hydrogens 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, 17, 12, 8, 8, 8, 8, 8, 8, 18, 18, 33, 33, 33, 33, 8, 8, 6, 1, 6, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 22, 22, 22, 17, 17, 12, 12, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 8, 8, 8, 8, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 455) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COCC[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456984388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456984388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001456984388 none COCC[C@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 6, 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, 7, 7, 7] 0 hydrogens 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, 9, 5, 5, 5, 5, 5, 5, 10, 10, 27, 27, 27, 27, 5, 5, 4, 1, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 22, 22, 22, 15, 15, 9, 9, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456984388 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984388 Building ZINC001456984399 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456984399 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/456 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456984399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456984399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001456984399 none COCC[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 6, 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, 7, 7, 7] 0 hydrogens 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, 9, 6, 6, 6, 6, 6, 6, 14, 14, 31, 31, 31, 31, 6, 6, 6, 1, 6, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 21, 21, 21, 15, 15, 9, 9, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/457 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456984399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456984399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001456984399 none COCC[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 8, 4, 4, 4, 4, 4, 4, 10, 10, 20, 21, 21, 21, 4, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 25, 25, 15, 15, 8, 8, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 3, 1, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456984399 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399 Building ZINC001456984399 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001456984399 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 456) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COCC[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456984399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001456984399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001456984399 none COCC[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 6, 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, 7, 7, 7] 0 hydrogens 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, 9, 6, 6, 6, 6, 6, 6, 14, 14, 31, 31, 31, 31, 6, 6, 6, 1, 6, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 21, 21, 21, 15, 15, 9, 9, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 2, 1, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 457) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COCC[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001456984399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001456984399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001456984399 none COCC[C@@H]1CN(C(=O)OC(C)(C)C)CCN1C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 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, 6, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 8, 4, 4, 4, 4, 4, 4, 10, 10, 20, 21, 21, 21, 4, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 25, 25, 25, 15, 15, 8, 8, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 3, 1, 3] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001456984399 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001456984399 Building ZINC001457047345 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457047345 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/458 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2c(c(Br)nc2C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001457047345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457047345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001457047345 none O=C(N1CCn2c(c(Br)nc2C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 17, 8, 1, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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: [12, 2, 18, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 31, 31, 31, 31, 31, 3, 3, 3, 3] 36 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/459 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCn2c(c(Br)nc2C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001457047345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457047345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001457047345 none O=C(N1CCn2c(c(Br)nc2C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 17, 8, 1, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 4, 4, 1, 1, 4, 4, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4] 38 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457047345 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345 Building ZINC001457047345 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457047345 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 458) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCn2c(c(Br)nc2C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001457047345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457047345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001457047345 none O=C(N1CCn2c(c(Br)nc2C(F)(F)F)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 17, 8, 1, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 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: [12, 2, 18, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 3, 3, 1, 1, 3, 3, 31, 31, 31, 31, 31, 31, 3, 3, 3, 3] 36 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 459) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCn2c(c(Br)nc2C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001457047345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457047345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001457047345 none O=C(N1CCn2c(c(Br)nc2C(F)(F)F)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 1, 17, 8, 1, 5, 15, 15, 15, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [12, 2, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 4, 4, 1, 1, 4, 4, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4] 38 rigid atoms, others: [16, 17, 18] set([0, 1, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457047345 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457047345 Building ZINC001457126931 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457126931 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/460 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2cccc(Br)c2)cc1Cl) `ZINC001457126931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457126931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001457126931 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2cccc(Br)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', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 17, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 7, 7, 7, 15, 26, 26, 21, 26, 26, 26, 4, 4, 4, 10, 10, 10, 4, 4, 2, 4, 4, 7, 7, 7, 26, 26, 22, 26, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/461 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2cccc(Br)c2)cc1Cl) `ZINC001457126931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457126931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001457126931 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2cccc(Br)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', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 17, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 10, 10, 10, 16, 28, 28, 23, 28, 28, 28, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 10, 10, 10, 28, 28, 27, 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, 41]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457126931 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931 Building ZINC001457126931 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457126931 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 460) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2cccc(Br)c2)cc1Cl) `ZINC001457126931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457126931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001457126931 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2cccc(Br)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', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 17, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 7, 7, 7, 15, 26, 26, 21, 26, 26, 26, 4, 4, 4, 10, 10, 10, 4, 4, 2, 4, 4, 7, 7, 7, 26, 26, 22, 26, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 461) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2cccc(Br)c2)cc1Cl) `ZINC001457126931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457126931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001457126931 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](C)Oc2cccc(Br)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', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 17, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 10, 10, 10, 16, 28, 28, 23, 28, 28, 28, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 10, 10, 10, 28, 28, 27, 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, 41]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457126931 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126931 Building ZINC001457126942 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457126942 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/462 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2cccc(Br)c2)cc1Cl) `ZINC001457126942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457126942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001457126942 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2cccc(Br)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', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 17, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 10, 10, 10, 16, 28, 28, 28, 28, 28, 28, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 10, 10, 10, 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, 41]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/463 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2cccc(Br)c2)cc1Cl) `ZINC001457126942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457126942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001457126942 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2cccc(Br)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', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 17, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 7, 7, 7, 16, 26, 26, 26, 26, 26, 26, 4, 4, 4, 10, 10, 10, 4, 4, 2, 4, 4, 7, 7, 7, 26, 26, 26, 26, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457126942 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942 Building ZINC001457126942 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457126942 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 462) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2cccc(Br)c2)cc1Cl) `ZINC001457126942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457126942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001457126942 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2cccc(Br)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', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 17, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 10, 10, 10, 16, 28, 28, 28, 28, 28, 28, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 10, 10, 10, 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, 41]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 463) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2cccc(Br)c2)cc1Cl) `ZINC001457126942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457126942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001457126942 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](C)Oc2cccc(Br)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', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 12, 1, 1, 1, 1, 1, 17, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 7, 7, 7, 16, 26, 26, 26, 26, 26, 26, 4, 4, 4, 10, 10, 10, 4, 4, 2, 4, 4, 7, 7, 7, 26, 26, 26, 26, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457126942 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457126942 Building ZINC001457128646 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457128646 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/464 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(S(C)(=O)=O)c2)c2cc(F)ccc2F)c1) `ZINC001457128646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457128646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001457128646 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(S(C)(=O)=O)c2)c2cc(F)ccc2F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 20, 20, 10, 20, 20, 24, 24, 24, 20, 5, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 2, 6, 6, 3, 20, 20, 10, 24, 24, 24, 20, 8, 8, 8, 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]) total number of confs: 104 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/465 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(S(C)(=O)=O)c2)c2cc(F)ccc2F)c1) `ZINC001457128646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457128646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001457128646 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(S(C)(=O)=O)c2)c2cc(F)ccc2F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 21, 21, 10, 21, 21, 25, 25, 25, 21, 6, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 2, 6, 6, 3, 21, 21, 11, 25, 25, 25, 21, 9, 9, 9, 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]) total number of confs: 112 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457128646 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646 Building ZINC001457128646 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457128646 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 464) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(S(C)(=O)=O)c2)c2cc(F)ccc2F)c1) `ZINC001457128646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457128646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001457128646 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(S(C)(=O)=O)c2)c2cc(F)ccc2F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 20, 20, 10, 20, 20, 24, 24, 24, 20, 5, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 2, 6, 6, 3, 20, 20, 10, 24, 24, 24, 20, 8, 8, 8, 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]) total number of confs: 104 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 465) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(S(C)(=O)=O)c2)c2cc(F)ccc2F)c1) `ZINC001457128646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457128646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001457128646 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@@H](c2cccc(S(C)(=O)=O)c2)c2cc(F)ccc2F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 21, 21, 10, 21, 21, 25, 25, 25, 21, 6, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 2, 6, 6, 3, 21, 21, 11, 25, 25, 25, 21, 9, 9, 9, 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]) total number of confs: 112 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457128646 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128646 Building ZINC001457128648 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457128648 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/466 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(S(C)(=O)=O)c2)c2cc(F)ccc2F)c1) `ZINC001457128648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457128648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001457128648 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(S(C)(=O)=O)c2)c2cc(F)ccc2F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 21, 21, 10, 21, 21, 25, 25, 25, 21, 6, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 2, 6, 6, 3, 21, 21, 13, 25, 25, 25, 21, 9, 9, 9, 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]) total number of confs: 114 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/467 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(S(C)(=O)=O)c2)c2cc(F)ccc2F)c1) `ZINC001457128648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457128648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001457128648 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(S(C)(=O)=O)c2)c2cc(F)ccc2F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 20, 20, 10, 20, 20, 24, 24, 24, 20, 5, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 2, 6, 6, 3, 20, 20, 10, 24, 24, 24, 20, 8, 8, 8, 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]) total number of confs: 104 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457128648 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648 Building ZINC001457128648 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457128648 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 466) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(S(C)(=O)=O)c2)c2cc(F)ccc2F)c1) `ZINC001457128648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457128648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001457128648 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2cccc(S(C)(=O)=O)c2)c2cc(F)ccc2F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 6, 6, 21, 21, 10, 21, 21, 25, 25, 25, 21, 6, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 2, 6, 6, 3, 21, 21, 13, 25, 25, 25, 21, 9, 9, 9, 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]) total number of confs: 114 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 467) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(S(C)(=O)=O)c2)c2cc(F)ccc2F)c1) `ZINC001457128648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457128648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001457128648 none Cc1cccc([C@]([O-])([SiH3])C(=O)N[C@H](c2cccc(S(C)(=O)=O)c2)c2cc(F)ccc2F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 15, 1, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 20, 20, 10, 20, 20, 24, 24, 24, 20, 5, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 2, 6, 6, 3, 20, 20, 10, 24, 24, 24, 20, 8, 8, 8, 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]) total number of confs: 104 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457128648 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457128648 Building ZINC001457189732 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457189732 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/468 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1S(=O)(=O)CC) `ZINC001457189732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457189732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457189732 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1S(=O)(=O)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5] 9 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 24 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/469 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1S(=O)(=O)CC) `ZINC001457189732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457189732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457189732 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1S(=O)(=O)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5] 9 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 24 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457189732 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732 Building ZINC001457189732 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457189732 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 468) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1S(=O)(=O)CC) `ZINC001457189732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457189732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457189732 none CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1S(=O)(=O)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5] 9 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 24 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 469) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1S(=O)(=O)CC) `ZINC001457189732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457189732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457189732 none CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1S(=O)(=O)CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5] 9 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 24 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457189732 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457189732 Building ZINC001457195482 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457195482 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/470 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001457195482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457195482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001457195482 none O=C(NC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 32, 35, 35, 35, 35, 35, 32, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 35, 35, 35, 35, 35] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/471 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001457195482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457195482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001457195482 none O=C(NC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 18, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 30, 32, 32, 32, 32, 32, 30, 18, 18, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 32, 32, 32, 32, 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457195482 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482 Building ZINC001457195482 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457195482 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 470) grep: /scratch/xiaobo/6899/xaj-8058088.10/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]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001457195482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457195482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001457195482 none O=C(NC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 32, 35, 35, 35, 35, 35, 32, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 35, 35, 35, 35, 35] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 471) grep: /scratch/xiaobo/6899/xaj-8058088.10/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]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001457195482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457195482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001457195482 none O=C(NC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 18, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 30, 32, 32, 32, 32, 32, 30, 18, 18, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 32, 32, 32, 32, 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457195482 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195482 Building ZINC001457195485 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457195485 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/472 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001457195485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457195485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001457195485 none O=C(NC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 18, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 31, 33, 33, 33, 33, 33, 31, 18, 18, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 33, 33, 33, 33, 33] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/473 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001457195485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457195485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001457195485 none O=C(NC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 15, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 35, 36, 36, 36, 36, 36, 35, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 36, 36, 36, 36, 36] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457195485 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485 Building ZINC001457195485 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457195485 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 472) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001457195485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457195485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001457195485 none O=C(NC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 18, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 31, 33, 33, 33, 33, 33, 31, 18, 18, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 33, 33, 33, 33, 33] 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]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 473) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1) `ZINC001457195485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457195485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001457195485 none O=C(NC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1)c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 1, 1, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 15, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 35, 36, 36, 36, 36, 36, 35, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 36, 36, 36, 36, 36] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457195485 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457195485 Building ZINC001457266928 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457266928 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/474 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1cc(Oc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2C)ccn1) `ZINC001457266928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457266928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001457266928 none CNC(=O)c1cc(Oc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2C)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 27, 27, 27, 27, 16, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 27, 27] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/475 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1cc(Oc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2C)ccn1) `ZINC001457266928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457266928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001457266928 none CNC(=O)c1cc(Oc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2C)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 28, 28, 28, 17, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 28, 28] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457266928 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928 Building ZINC001457266928 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457266928 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 474) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CNC(=O)c1cc(Oc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2C)ccn1) `ZINC001457266928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457266928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001457266928 none CNC(=O)c1cc(Oc2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2C)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [27, 27, 27, 27, 27, 27, 16, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 6, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 27, 27] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 475) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CNC(=O)c1cc(Oc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2C)ccn1) `ZINC001457266928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457266928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001457266928 none CNC(=O)c1cc(Oc2cc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)ccc2C)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.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', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 5, 1, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 28, 28, 28, 17, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 28, 28] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457266928 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457266928 Building ZINC001457337837 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457337837 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/476 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2c(cc1Br)N(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@H](C)O2) `ZINC001457337837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457337837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457337837 none Cc1cc2c(cc1Br)N(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@H](C)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', '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, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 13, 13, 13, 13, 13, 13, 10, 2, 10, 1, 1, 1, 10, 10, 10, 10, 19, 19, 13, 19, 19, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 19, 19, 13, 19, 19, 10, 13, 13, 13, 13, 13] 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/477 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/477' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2c(cc1Br)N(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@H](C)O2) `ZINC001457337837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457337837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457337837 none Cc1cc2c(cc1Br)N(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@H](C)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', '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, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 18, 18, 18, 18, 18, 18, 18, 14, 2, 14, 1, 1, 1, 9, 9, 9, 9, 17, 17, 9, 17, 17, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 17, 17, 9, 17, 17, 9, 18, 18, 18, 18, 18] 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457337837 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837 Building ZINC001457337837 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457337837 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 476) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cc2c(cc1Br)N(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@H](C)O2) `ZINC001457337837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457337837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457337837 none Cc1cc2c(cc1Br)N(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@H](C)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', '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, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 13, 13, 13, 13, 13, 13, 10, 2, 10, 1, 1, 1, 10, 10, 10, 10, 19, 19, 13, 19, 19, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 19, 19, 13, 19, 19, 10, 13, 13, 13, 13, 13] 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 477) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cc2c(cc1Br)N(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@H](C)O2) `ZINC001457337837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457337837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457337837 none Cc1cc2c(cc1Br)N(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@H](C)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', '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, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 18, 18, 18, 18, 18, 18, 18, 14, 2, 14, 1, 1, 1, 9, 9, 9, 9, 17, 17, 9, 17, 17, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 17, 17, 9, 17, 17, 9, 18, 18, 18, 18, 18] 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: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457337837 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337837 Building ZINC001457337842 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457337842 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/478 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2c(cc1Br)N(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@@H](C)O2) `ZINC001457337842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457337842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457337842 none Cc1cc2c(cc1Br)N(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@@H](C)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', '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, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 18, 18, 18, 18, 18, 18, 18, 14, 3, 14, 1, 1, 1, 9, 9, 9, 9, 18, 18, 9, 18, 18, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 18, 18, 18, 18, 18, 9, 18, 18, 18, 18, 18] 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/479 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc2c(cc1Br)N(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@@H](C)O2) `ZINC001457337842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457337842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457337842 none Cc1cc2c(cc1Br)N(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@@H](C)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', '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, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 16, 16, 16, 16, 16, 16, 13, 3, 13, 1, 1, 1, 9, 9, 9, 9, 18, 18, 9, 18, 18, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 18, 18, 9, 18, 18, 9, 16, 16, 16, 16, 16] 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457337842 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842 Building ZINC001457337842 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457337842 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 478) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cc2c(cc1Br)N(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@@H](C)O2) `ZINC001457337842.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457337842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457337842 none Cc1cc2c(cc1Br)N(C(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@@H](C)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', '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, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 18, 18, 18, 18, 18, 18, 18, 14, 3, 14, 1, 1, 1, 9, 9, 9, 9, 18, 18, 9, 18, 18, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 18, 18, 18, 18, 18, 9, 18, 18, 18, 18, 18] 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 479) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cc2c(cc1Br)N(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@@H](C)O2) `ZINC001457337842.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457337842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001457337842 none Cc1cc2c(cc1Br)N(C(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)C[C@@H](C)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', '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, 1, 1, 1, 1, 1, 1, 17, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 16, 16, 16, 16, 16, 16, 13, 3, 13, 1, 1, 1, 9, 9, 9, 9, 18, 18, 9, 18, 18, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 18, 18, 9, 18, 18, 9, 16, 16, 16, 16, 16] 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: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457337842 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457337842 Building ZINC001457413049 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457413049 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/480 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@](O)(c1ccccc1Cl)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001457413049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457413049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001457413049 none O=C(NC[C@@](O)(c1ccccc1Cl)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 16, 27, 27, 30, 30, 30, 30, 30, 30, 25, 27, 27, 27, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 16, 16, 81, 30, 30, 30, 30, 7, 7, 7, 7] 150 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]) total number of confs: 221 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/481 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@](O)(c1ccccc1Cl)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001457413049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457413049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001457413049 none O=C(NC[C@@](O)(c1ccccc1Cl)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 16, 27, 27, 32, 32, 32, 32, 32, 32, 25, 27, 27, 27, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 16, 16, 81, 32, 32, 32, 32, 7, 7, 7, 7] 150 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]) total number of confs: 218 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457413049 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049 Building ZINC001457413049 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457413049 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 480) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@@](O)(c1ccccc1Cl)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001457413049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457413049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001457413049 none O=C(NC[C@@](O)(c1ccccc1Cl)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 16, 27, 27, 30, 30, 30, 30, 30, 30, 25, 27, 27, 27, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 16, 16, 81, 30, 30, 30, 30, 7, 7, 7, 7] 150 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]) total number of confs: 221 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 481) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@@](O)(c1ccccc1Cl)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001457413049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457413049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001457413049 none O=C(NC[C@@](O)(c1ccccc1Cl)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 16, 27, 27, 32, 32, 32, 32, 32, 32, 25, 27, 27, 27, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 16, 16, 81, 32, 32, 32, 32, 7, 7, 7, 7] 150 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]) total number of confs: 218 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457413049 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413049 Building ZINC001457413056 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457413056 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/482 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@](O)(c1ccccc1Cl)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001457413056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457413056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001457413056 none O=C(NC[C@](O)(c1ccccc1Cl)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 13, 25, 25, 31, 31, 29, 31, 31, 31, 25, 25, 25, 25, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 13, 13, 75, 31, 31, 31, 31, 7, 7, 7, 7] 150 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]) total number of confs: 209 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/483 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@](O)(c1ccccc1Cl)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001457413056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457413056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001457413056 none O=C(NC[C@](O)(c1ccccc1Cl)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 14, 25, 25, 30, 30, 29, 30, 30, 30, 25, 25, 25, 25, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 14, 14, 75, 30, 30, 30, 30, 7, 7, 7, 7] 150 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]) total number of confs: 199 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457413056 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056 Building ZINC001457413056 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457413056 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 482) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@](O)(c1ccccc1Cl)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001457413056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457413056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001457413056 none O=C(NC[C@](O)(c1ccccc1Cl)C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 13, 25, 25, 31, 31, 29, 31, 31, 31, 25, 25, 25, 25, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 13, 13, 75, 31, 31, 31, 31, 7, 7, 7, 7] 150 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]) total number of confs: 209 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 483) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@](O)(c1ccccc1Cl)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001457413056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457413056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001457413056 none O=C(NC[C@](O)(c1ccccc1Cl)C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 14, 25, 25, 30, 30, 29, 30, 30, 30, 25, 25, 25, 25, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 14, 14, 75, 30, 30, 30, 30, 7, 7, 7, 7] 150 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]) total number of confs: 199 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457413056 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457413056 Building ZINC001457419186 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457419186 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/484 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1c1ccc(Br)cc1) `ZINC001457419186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457419186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001457419186 none Cc1[nH]nc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', '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.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: [5, 1, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 20, 20, 20, 9, 13, 13, 18, 18, 13, 17, 18, 18, 13, 13, 13, 4, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/485 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1c1ccc(Br)cc1) `ZINC001457419186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457419186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001457419186 none Cc1[nH]nc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', '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.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: [5, 1, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 17, 17, 17, 9, 13, 13, 19, 19, 13, 17, 19, 19, 13, 13, 13, 4, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457419186 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186 Building ZINC001457419186 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457419186 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 484) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1[nH]nc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1c1ccc(Br)cc1) `ZINC001457419186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457419186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001457419186 none Cc1[nH]nc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', '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.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: [5, 1, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 20, 20, 20, 9, 13, 13, 18, 18, 13, 17, 18, 18, 13, 13, 13, 4, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 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, 41, 42, 43, 44, 45, 46]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 485) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1[nH]nc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1c1ccc(Br)cc1) `ZINC001457419186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457419186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001457419186 none Cc1[nH]nc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', '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.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: [5, 1, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 1, 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, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 17, 17, 17, 9, 13, 13, 19, 19, 13, 17, 19, 19, 13, 13, 13, 4, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457419186 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457419186 Building ZINC001457423363 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457423363 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/486 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/486' -> `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)Nc1[nH]nc(C(F)(F)F)c1c1ccc(Cl)cc1) `ZINC001457423363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457423363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457423363 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1[nH]nc(C(F)(F)F)c1c1ccc(Cl)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.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 6, 8, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 45, 45, 38, 38, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 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]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/487 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/487' -> `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)Nc1[nH]nc(C(F)(F)F)c1c1ccc(Cl)cc1) `ZINC001457423363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457423363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457423363 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1[nH]nc(C(F)(F)F)c1c1ccc(Cl)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.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 6, 8, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 46, 46, 38, 38, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457423363 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363 Building ZINC001457423363 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457423363 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 486) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1[nH]nc(C(F)(F)F)c1c1ccc(Cl)cc1) `ZINC001457423363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457423363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457423363 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1[nH]nc(C(F)(F)F)c1c1ccc(Cl)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.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 6, 8, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 45, 45, 38, 38, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 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]) total number of confs: 123 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 487) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1[nH]nc(C(F)(F)F)c1c1ccc(Cl)cc1) `ZINC001457423363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457423363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457423363 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1[nH]nc(C(F)(F)F)c1c1ccc(Cl)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.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 6, 8, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 46, 46, 38, 38, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457423363 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457423363 Building ZINC001457510357 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457510357 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/488 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)sc1c1nnc(S)n1C) `ZINC001457510357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457510357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001457510357 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)sc1c1nnc(S)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 1, 8, 8, 1, 14, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 11, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 11, 11, 11, 34, 34, 34, 34, 34, 34, 11, 11, 11, 6, 6, 1, 6, 102, 34, 34, 34] 150 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]) total number of confs: 169 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/489 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)sc1c1nnc(S)n1C) `ZINC001457510357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457510357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001457510357 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)sc1c1nnc(S)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 1, 8, 8, 1, 14, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 11, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 11, 11, 11, 35, 35, 35, 35, 35, 35, 11, 11, 11, 6, 6, 1, 6, 105, 35, 35, 35] 150 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]) total number of confs: 174 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457510357 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357 Building ZINC001457510357 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457510357 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 488) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)sc1c1nnc(S)n1C) `ZINC001457510357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457510357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001457510357 none Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)sc1c1nnc(S)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 1, 8, 8, 1, 14, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 11, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 11, 11, 11, 34, 34, 34, 34, 34, 34, 11, 11, 11, 6, 6, 1, 6, 102, 34, 34, 34] 150 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]) total number of confs: 169 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 489) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)sc1c1nnc(S)n1C) `ZINC001457510357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457510357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001457510357 none Cc1nc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)sc1c1nnc(S)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 14, 1, 1, 8, 8, 1, 14, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 11, 6, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 11, 11, 11, 35, 35, 35, 35, 35, 35, 11, 11, 11, 6, 6, 1, 6, 105, 35, 35, 35] 150 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]) total number of confs: 174 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457510357 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457510357 Building ZINC001457514017 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457514017 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/490 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2ccc(Cl)cc2)C1=O) `ZINC001457514017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457514017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457514017 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2ccc(Cl)cc2)C1=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', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', '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, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 18, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 18, 18, 27, 27, 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/491 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2ccc(Cl)cc2)C1=O) `ZINC001457514017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457514017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457514017 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2ccc(Cl)cc2)C1=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', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', '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, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 19, 19, 27, 27, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457514017 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017 Building ZINC001457514017 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457514017 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 490) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2ccc(Cl)cc2)C1=O) `ZINC001457514017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457514017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457514017 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2ccc(Cl)cc2)C1=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', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', '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, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 18, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 3, 18, 18, 27, 27, 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]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 491) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2ccc(Cl)cc2)C1=O) `ZINC001457514017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457514017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001457514017 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCCN1C(=O)S/C(=C/c2ccc(Cl)cc2)C1=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', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', '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, 8, 1, 11, 14, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 19, 19, 27, 27, 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]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457514017 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457514017 Building ZINC001457785599 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457785599 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/492 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cc(Cl)cc(Cl)c1)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001457785599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457785599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001457785599 none CCOC(=O)[C@H](Cc1cc(Cl)cc(Cl)c1)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 28, 10, 28, 3, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 44, 44, 44, 44, 44, 25, 25, 25, 25, 25, 3, 2, 2, 2, 2, 2, 2] 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]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/493 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cc(Cl)cc(Cl)c1)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001457785599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457785599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001457785599 none CCOC(=O)[C@H](Cc1cc(Cl)cc(Cl)c1)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 33, 32, 13, 32, 3, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 44, 44, 44, 44, 44, 27, 27, 27, 27, 27, 3, 2, 2, 2, 2, 2, 2] 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]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457785599 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599 Building ZINC001457785599 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457785599 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 492) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)[C@H](Cc1cc(Cl)cc(Cl)c1)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001457785599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457785599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001457785599 none CCOC(=O)[C@H](Cc1cc(Cl)cc(Cl)c1)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 28, 10, 28, 3, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 44, 44, 44, 44, 44, 25, 25, 25, 25, 25, 3, 2, 2, 2, 2, 2, 2] 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]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 493) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)[C@H](Cc1cc(Cl)cc(Cl)c1)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001457785599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457785599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001457785599 none CCOC(=O)[C@H](Cc1cc(Cl)cc(Cl)c1)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 33, 32, 13, 32, 3, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 44, 44, 44, 44, 44, 27, 27, 27, 27, 27, 3, 2, 2, 2, 2, 2, 2] 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]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457785599 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785599 Building ZINC001457785602 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457785602 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/494 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](Cc1cc(Cl)cc(Cl)c1)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001457785602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457785602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001457785602 none CCOC(=O)[C@@H](Cc1cc(Cl)cc(Cl)c1)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 33, 32, 13, 32, 3, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 44, 44, 44, 44, 44, 27, 27, 27, 27, 27, 3, 2, 2, 2, 2, 2, 2] 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]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/495 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](Cc1cc(Cl)cc(Cl)c1)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001457785602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457785602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001457785602 none CCOC(=O)[C@@H](Cc1cc(Cl)cc(Cl)c1)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 29, 28, 10, 28, 3, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 43, 43, 43, 43, 43, 26, 26, 26, 26, 26, 3, 2, 2, 2, 2, 2, 2] 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]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457785602 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602 Building ZINC001457785602 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457785602 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 494) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)[C@@H](Cc1cc(Cl)cc(Cl)c1)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001457785602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457785602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001457785602 none CCOC(=O)[C@@H](Cc1cc(Cl)cc(Cl)c1)NC(=O)[C@@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 33, 32, 13, 32, 3, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 44, 44, 44, 44, 44, 27, 27, 27, 27, 27, 3, 2, 2, 2, 2, 2, 2] 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]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 495) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)[C@@H](Cc1cc(Cl)cc(Cl)c1)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C) `ZINC001457785602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457785602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001457785602 none CCOC(=O)[C@@H](Cc1cc(Cl)cc(Cl)c1)NC(=O)[C@]([O-])([SiH3])c1cc(F)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 29, 28, 10, 28, 3, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 43, 43, 43, 43, 43, 26, 26, 26, 26, 26, 3, 2, 2, 2, 2, 2, 2] 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]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457785602 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457785602 Building ZINC001457790748 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457790748 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/496 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(O)c(Br)cc2Br)cn1) `ZINC001457790748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457790748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001457790748 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(O)c(Br)cc2Br)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.2', 'N.2', '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, 12, 1, 17, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [24, 11, 24, 24, 11, 11, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 4, 13, 26, 13, 11] 100 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/497 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cc(O)c(Br)cc2Br)cn1) `ZINC001457790748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457790748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001457790748 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cc(O)c(Br)cc2Br)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.2', 'N.2', '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, 12, 1, 17, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [24, 10, 24, 24, 10, 10, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 5, 15, 30, 15, 10] 100 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457790748 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748 Building ZINC001457790748 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457790748 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 496) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(O)c(Br)cc2Br)cn1) `ZINC001457790748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457790748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001457790748 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cc(O)c(Br)cc2Br)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.2', 'N.2', '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, 12, 1, 17, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [24, 11, 24, 24, 11, 11, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 4, 13, 26, 13, 11] 100 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 497) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cc(O)c(Br)cc2Br)cn1) `ZINC001457790748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457790748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001457790748 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cc(O)c(Br)cc2Br)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.2', 'N.2', '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, 12, 1, 17, 1, 1, 17, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [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] 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: [24, 10, 24, 24, 10, 10, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 5, 15, 30, 15, 10] 100 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457790748 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457790748 Building ZINC001457802942 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457802942 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/498 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](Cc1ccccc1Br)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001457802942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457802942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001457802942 none CC[C@@H](Cc1ccccc1Br)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 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: [11, 8, 2, 8, 8, 17, 26, 26, 17, 26, 26, 26, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 9, 9, 7, 9, 9, 7, 13, 13, 13, 13, 13, 17, 17, 26, 26, 23, 26, 2, 7, 9, 9, 7, 9, 9, 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/499 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](Cc1ccccc1Br)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001457802942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457802942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001457802942 none CC[C@@H](Cc1ccccc1Br)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 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: [13, 12, 4, 12, 12, 21, 26, 26, 21, 26, 26, 26, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 16, 16, 16, 16, 16, 21, 21, 26, 26, 25, 26, 4, 6, 8, 8, 8, 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: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457802942 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942 Building ZINC001457802942 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457802942 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 498) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@@H](Cc1ccccc1Br)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001457802942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457802942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001457802942 none CC[C@@H](Cc1ccccc1Br)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 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: [11, 8, 2, 8, 8, 17, 26, 26, 17, 26, 26, 26, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 9, 9, 7, 9, 9, 7, 13, 13, 13, 13, 13, 17, 17, 26, 26, 23, 26, 2, 7, 9, 9, 7, 9, 9, 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: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 499) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@@H](Cc1ccccc1Br)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001457802942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457802942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001457802942 none CC[C@@H](Cc1ccccc1Br)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 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: [13, 12, 4, 12, 12, 21, 26, 26, 21, 26, 26, 26, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 16, 16, 16, 16, 16, 21, 21, 26, 26, 25, 26, 4, 6, 8, 8, 8, 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: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457802942 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802942 Building ZINC001457802943 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457802943 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/500 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](Cc1ccccc1Br)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001457802943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457802943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001457802943 none CC[C@H](Cc1ccccc1Br)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 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: [13, 11, 4, 11, 11, 21, 26, 26, 21, 26, 26, 26, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 15, 15, 15, 15, 15, 21, 21, 26, 26, 25, 26, 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: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/501 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](Cc1ccccc1Br)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001457802943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457802943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001457802943 none CC[C@H](Cc1ccccc1Br)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 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: [12, 9, 3, 9, 9, 18, 27, 27, 18, 27, 27, 27, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 14, 14, 14, 14, 14, 18, 18, 27, 27, 24, 27, 3, 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: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457802943 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943 Building ZINC001457802943 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457802943 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 500) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@H](Cc1ccccc1Br)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001457802943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457802943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001457802943 none CC[C@H](Cc1ccccc1Br)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 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: [13, 11, 4, 11, 11, 21, 26, 26, 21, 26, 26, 26, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 15, 15, 15, 15, 15, 21, 21, 26, 26, 25, 26, 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: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 501) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@H](Cc1ccccc1Br)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001457802943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457802943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001457802943 none CC[C@H](Cc1ccccc1Br)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 5, 7, 5, 1, 1, 1, 1, 1, 1, 17, 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: [12, 9, 3, 9, 9, 18, 27, 27, 18, 27, 27, 27, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 14, 14, 14, 14, 14, 18, 18, 27, 27, 24, 27, 3, 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: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457802943 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457802943 Building ZINC001457851587 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001457851587 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/502 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001457851587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457851587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457851587 none CCCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 8, 8, 8, 10, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 10, 8, 8, 4, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 49] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 84 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/503 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001457851587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457851587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457851587 none CCCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 8, 8, 8, 10, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 10, 8, 8, 4, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 49] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 84 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/504 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/504' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001457851587.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001457851587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457851587 none CCCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 7, 7, 7, 10, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 9, 9, 10, 10, 10, 10, 10, 7, 7, 4, 4, 4, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/505 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/505' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001457851587.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001457851587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457851587 none CCCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 7, 7, 7, 10, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 9, 9, 10, 10, 10, 10, 10, 7, 7, 4, 4, 4, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457851587 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 Building ZINC001457851587 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001457851587 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 502) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001457851587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457851587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457851587 none CCCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 8, 8, 8, 10, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 10, 8, 8, 4, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 49] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 84 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 503) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001457851587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457851587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457851587 none CCCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 8, 8, 8, 10, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 10, 8, 8, 4, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 49] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 84 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 504) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001457851587.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001457851587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457851587 none CCCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 7, 7, 7, 10, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 9, 9, 10, 10, 10, 10, 10, 7, 7, 4, 4, 4, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 505) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001457851587.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001457851587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457851587 none CCCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 7, 7, 7, 10, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 9, 9, 10, 10, 10, 10, 10, 7, 7, 4, 4, 4, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457851587 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 Building ZINC001457851587 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001457851587 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 502) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001457851587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457851587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457851587 none CCCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 8, 8, 8, 10, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 10, 8, 8, 4, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 49] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 84 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 503) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001457851587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457851587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457851587 none CCCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 8, 8, 8, 10, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 10, 8, 8, 4, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 49] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 84 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 504) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001457851587.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001457851587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457851587 none CCCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 7, 7, 7, 10, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 9, 9, 10, 10, 10, 10, 10, 7, 7, 4, 4, 4, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 505) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001457851587.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001457851587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457851587 none CCCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 7, 7, 7, 10, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 9, 9, 10, 10, 10, 10, 10, 7, 7, 4, 4, 4, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457851587 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 Building ZINC001457851587 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001457851587 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 502) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001457851587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457851587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457851587 none CCCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 8, 8, 8, 10, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 10, 8, 8, 4, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 49] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 84 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 503) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001457851587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457851587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457851587 none CCCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 8, 8, 8, 10, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 10, 10, 10, 10, 10, 10, 10, 8, 8, 4, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 49] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 84 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 504) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001457851587.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001457851587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457851587 none CCCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 7, 7, 7, 10, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 9, 9, 10, 10, 10, 10, 10, 7, 7, 4, 4, 4, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 505) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001457851587.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001457851587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001457851587 none CCCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 7, 7, 7, 10, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 9, 9, 10, 10, 10, 10, 10, 7, 7, 4, 4, 4, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457851587 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457851587 Building ZINC001457858334 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001457858334 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/506 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(C)C1) `ZINC001457858334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457858334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457858334 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 8, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 7, 8, 2, 2, 2, 2, 7, 7, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/507 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(C)C1) `ZINC001457858334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457858334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457858334 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 9, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 8, 8, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/508 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/508' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(C)C1) `ZINC001457858334.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001457858334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457858334 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 8, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 7, 8, 2, 2, 2, 2, 7, 7, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/509 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/509' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(C)C1) `ZINC001457858334.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001457858334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457858334 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 9, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 8, 8, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457858334 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 Building ZINC001457858334 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001457858334 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 506) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(C)C1) `ZINC001457858334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457858334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457858334 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 8, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 7, 8, 2, 2, 2, 2, 7, 7, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 507) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(C)C1) `ZINC001457858334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457858334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457858334 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 9, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 8, 8, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 508) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(C)C1) `ZINC001457858334.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001457858334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457858334 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 8, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 7, 8, 2, 2, 2, 2, 7, 7, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 509) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(C)C1) `ZINC001457858334.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001457858334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457858334 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 9, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 8, 8, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457858334 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 Building ZINC001457858334 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001457858334 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 506) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(C)C1) `ZINC001457858334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457858334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457858334 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 8, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 7, 8, 2, 2, 2, 2, 7, 7, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 507) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(C)C1) `ZINC001457858334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457858334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457858334 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 9, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 8, 8, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 508) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(C)C1) `ZINC001457858334.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001457858334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457858334 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 8, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 7, 8, 2, 2, 2, 2, 7, 7, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 509) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(C)C1) `ZINC001457858334.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001457858334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457858334 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 9, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 8, 8, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457858334 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 Building ZINC001457858334 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001457858334 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 506) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(C)C1) `ZINC001457858334.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457858334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457858334 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 8, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 7, 8, 2, 2, 2, 2, 7, 7, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 507) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(C)C1) `ZINC001457858334.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457858334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457858334 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 9, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 8, 8, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 508) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(C)C1) `ZINC001457858334.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001457858334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457858334 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 8, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 7, 8, 2, 2, 2, 2, 7, 7, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 509) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(C)C1) `ZINC001457858334.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001457858334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457858334 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 9, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 8, 8, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457858334 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457858334 Building ZINC001457859995 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001457859995 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/510 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(C)C1) `ZINC001457859995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457859995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457859995 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 10, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 11, 11, 11, 11, 3, 3, 3, 2, 9, 9, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/511 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(C)C1) `ZINC001457859995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457859995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457859995 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 7, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 12, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/512 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/512' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(C)C1) `ZINC001457859995.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001457859995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457859995 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 10, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 11, 11, 11, 11, 3, 3, 3, 2, 9, 9, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/513 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/513' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(C)C1) `ZINC001457859995.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001457859995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457859995 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 7, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 12, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457859995 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 Building ZINC001457859995 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001457859995 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 510) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(C)C1) `ZINC001457859995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457859995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457859995 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 10, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 11, 11, 11, 11, 3, 3, 3, 2, 9, 9, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 511) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(C)C1) `ZINC001457859995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457859995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457859995 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 7, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 12, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 512) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(C)C1) `ZINC001457859995.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001457859995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457859995 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 10, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 11, 11, 11, 11, 3, 3, 3, 2, 9, 9, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 513) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(C)C1) `ZINC001457859995.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001457859995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457859995 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 7, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 12, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457859995 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 Building ZINC001457859995 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001457859995 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 510) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(C)C1) `ZINC001457859995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457859995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457859995 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 10, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 11, 11, 11, 11, 3, 3, 3, 2, 9, 9, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 511) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(C)C1) `ZINC001457859995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457859995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457859995 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 7, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 12, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 512) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(C)C1) `ZINC001457859995.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001457859995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457859995 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 10, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 11, 11, 11, 11, 3, 3, 3, 2, 9, 9, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 513) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(C)C1) `ZINC001457859995.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001457859995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457859995 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 7, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 12, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457859995 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 Building ZINC001457859995 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001457859995 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 510) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(C)C1) `ZINC001457859995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457859995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457859995 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 10, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 11, 11, 11, 11, 3, 3, 3, 2, 9, 9, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 511) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(C)C1) `ZINC001457859995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457859995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457859995 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 7, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 12, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 512) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(C)C1) `ZINC001457859995.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001457859995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457859995 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 10, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 11, 11, 11, 11, 3, 3, 3, 2, 9, 9, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 513) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(C)C1) `ZINC001457859995.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001457859995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001457859995 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@H]1CCCN(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 7, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 12, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 9, 9, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457859995 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457859995 Building ZINC001457930173 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457930173 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/514 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2ccc(O)cc2C1) `ZINC001457930173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457930173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001457930173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2ccc(O)cc2C1 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.3', 'F', 'F', 'F', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 5, 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, 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] 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: [3, 3, 3, 3, 3, 28, 28, 3, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 28, 28, 3, 28, 3, 3, 3, 6, 6, 6, 6, 12, 6, 6, 6] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 85 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/515 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/515' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2ccc(O)cc2C1) `ZINC001457930173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457930173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001457930173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2ccc(O)cc2C1 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.3', 'F', 'F', 'F', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 5, 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, 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] 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: [3, 3, 3, 3, 3, 28, 28, 3, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 28, 28, 3, 28, 3, 3, 3, 6, 6, 6, 6, 12, 6, 6, 6] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 85 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457930173 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173 Building ZINC001457930173 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457930173 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 514) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2ccc(O)cc2C1) `ZINC001457930173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457930173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001457930173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1Cc2ccc(O)cc2C1 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.3', 'F', 'F', 'F', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 5, 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, 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] 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: [3, 3, 3, 3, 3, 28, 28, 3, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 28, 28, 3, 28, 3, 3, 3, 6, 6, 6, 6, 12, 6, 6, 6] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 85 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 515) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2ccc(O)cc2C1) `ZINC001457930173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457930173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001457930173 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1Cc2ccc(O)cc2C1 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.3', 'F', 'F', 'F', 'C.ar', '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', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 5, 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, 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] 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: [3, 3, 3, 3, 3, 28, 28, 3, 28, 28, 28, 28, 28, 28, 3, 3, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 28, 28, 3, 28, 3, 3, 3, 6, 6, 6, 6, 12, 6, 6, 6] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 85 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457930173 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457930173 Building ZINC001457981824 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457981824 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/516 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(OC)cc1OC) `ZINC001457981824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457981824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001457981824 none COC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(OC)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 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, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [34, 34, 16, 34, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 8, 8, 7, 8, 13, 8, 8, 8, 10, 34, 34, 34, 16, 16, 4, 3, 1, 3, 8, 8, 13, 13, 13, 8, 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]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/517 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(OC)cc1OC) `ZINC001457981824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457981824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001457981824 none COC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(OC)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 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, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [35, 35, 15, 35, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 10, 10, 7, 10, 16, 10, 10, 10, 12, 35, 35, 35, 15, 15, 4, 3, 1, 3, 10, 10, 16, 16, 16, 10, 12, 12, 12] 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: 165 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457981824 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824 Building ZINC001457981824 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457981824 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 516) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(OC)cc1OC) `ZINC001457981824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457981824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001457981824 none COC(=O)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(OC)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 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, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [34, 34, 16, 34, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 8, 8, 7, 8, 13, 8, 8, 8, 10, 34, 34, 34, 16, 16, 4, 3, 1, 3, 8, 8, 13, 13, 13, 8, 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]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 517) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(OC)cc1OC) `ZINC001457981824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457981824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001457981824 none COC(=O)C[C@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(OC)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 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, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [35, 35, 15, 35, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 10, 10, 7, 10, 16, 10, 10, 10, 12, 35, 35, 35, 15, 15, 4, 3, 1, 3, 10, 10, 16, 16, 16, 10, 12, 12, 12] 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: 165 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457981824 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981824 Building ZINC001457981830 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457981830 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/518 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(OC)cc1OC) `ZINC001457981830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457981830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001457981830 none COC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(OC)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 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, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 15, 36, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 10, 10, 7, 10, 15, 10, 10, 10, 12, 36, 36, 36, 15, 15, 4, 3, 1, 3, 10, 10, 15, 15, 15, 10, 12, 12, 12] 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: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/519 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(OC)cc1OC) `ZINC001457981830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457981830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001457981830 none COC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(OC)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 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, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [34, 34, 16, 34, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 8, 8, 7, 8, 12, 8, 8, 8, 10, 34, 34, 34, 16, 16, 4, 3, 1, 3, 8, 8, 12, 12, 12, 8, 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]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457981830 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830 Building ZINC001457981830 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001457981830 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 518) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(OC)cc1OC) `ZINC001457981830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001457981830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001457981830 none COC(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(OC)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 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, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 15, 36, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 10, 10, 7, 10, 15, 10, 10, 10, 12, 36, 36, 36, 15, 15, 4, 3, 1, 3, 10, 10, 15, 15, 15, 10, 12, 12, 12] 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: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 519) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(OC)cc1OC) `ZINC001457981830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001457981830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001457981830 none COC(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)c1ccc(OC)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 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, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 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: [34, 34, 16, 34, 6, 4, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 6, 8, 8, 7, 8, 12, 8, 8, 8, 10, 34, 34, 34, 16, 16, 4, 3, 1, 3, 8, 8, 12, 12, 12, 8, 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]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001457981830 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001457981830 Building ZINC001458027813 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458027813 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/520 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC[C@@H]1O) `ZINC001458027813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458027813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001458027813 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC[C@@H]1O 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 48] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/521 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC[C@@H]1O) `ZINC001458027813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458027813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001458027813 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC[C@@H]1O 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 13, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 8, 8, 7, 8, 2, 2, 2, 2, 11, 11, 17, 17, 19, 19, 19, 19, 19, 19, 19, 19, 57] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458027813 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813 Building ZINC001458027813 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458027813 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 520) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC[C@@H]1O) `ZINC001458027813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458027813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001458027813 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC[C@@H]1O 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 48] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 521) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC[C@@H]1O) `ZINC001458027813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458027813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001458027813 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC[C@@H]1CCCC[C@@H]1O 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 13, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 8, 8, 7, 8, 2, 2, 2, 2, 11, 11, 17, 17, 19, 19, 19, 19, 19, 19, 19, 19, 57] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458027813 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458027813 Building ZINC001458038734 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458038734 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/522 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@]2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1O2) `ZINC001458038734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458038734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001458038734 none CC(C)(C)OC(=O)N1CC[C@@]2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 17, 31, 17, 17, 17, 17, 17, 17, 10, 17, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 17, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 4, 2, 2, 1, 2, 2, 17, 17, 17, 17] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/523 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@]2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1O2) `ZINC001458038734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458038734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001458038734 none CC(C)(C)OC(=O)N1CC[C@@]2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 30, 16, 30, 16, 16, 16, 16, 16, 16, 10, 16, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 16, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 16, 16, 4, 3, 3, 1, 3, 3, 16, 16, 16, 16] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458038734 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734 Building ZINC001458038734 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458038734 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 522) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@@]2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1O2) `ZINC001458038734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458038734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001458038734 none CC(C)(C)OC(=O)N1CC[C@@]2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 17, 31, 17, 17, 17, 17, 17, 17, 10, 17, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 17, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 4, 2, 2, 1, 2, 2, 17, 17, 17, 17] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 523) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@@]2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1O2) `ZINC001458038734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458038734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001458038734 none CC(C)(C)OC(=O)N1CC[C@@]2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 30, 16, 30, 16, 16, 16, 16, 16, 16, 10, 16, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 16, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 16, 16, 4, 3, 3, 1, 3, 3, 16, 16, 16, 16] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458038734 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038734 Building ZINC001458038738 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458038738 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/524 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@]2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1O2) `ZINC001458038738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458038738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001458038738 none CC(C)(C)OC(=O)N1CC[C@@]2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 30, 17, 30, 17, 17, 17, 17, 17, 17, 7, 17, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 17, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 4, 2, 2, 1, 2, 2, 17, 17, 17, 17] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/525 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@]2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1O2) `ZINC001458038738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458038738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001458038738 none CC(C)(C)OC(=O)N1CC[C@@]2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 28, 15, 28, 15, 15, 15, 15, 15, 15, 7, 15, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 15, 15, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 4, 3, 3, 1, 3, 3, 15, 15, 15, 15] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458038738 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738 Building ZINC001458038738 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458038738 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 524) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/524: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@]2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1O2) `ZINC001458038738.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458038738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001458038738 none CC(C)(C)OC(=O)N1CC[C@@]2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 30, 17, 30, 17, 17, 17, 17, 17, 17, 7, 17, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 17, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 4, 2, 2, 1, 2, 2, 17, 17, 17, 17] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 525) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/525: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@]2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1O2) `ZINC001458038738.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458038738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001458038738 none CC(C)(C)OC(=O)N1CC[C@@]2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 28, 15, 28, 15, 15, 15, 15, 15, 15, 7, 15, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 15, 15, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 4, 3, 3, 1, 3, 3, 15, 15, 15, 15] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458038738 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038738 Building ZINC001458038742 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458038742 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/526 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@]2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1O2) `ZINC001458038742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458038742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001458038742 none CC(C)(C)OC(=O)N1CC[C@]2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 26, 15, 26, 15, 15, 15, 15, 15, 15, 12, 15, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 15, 15, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 4, 3, 3, 1, 3, 3, 15, 15, 15, 15] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/527 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@]2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1O2) `ZINC001458038742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458038742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001458038742 none CC(C)(C)OC(=O)N1CC[C@]2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 30, 18, 30, 18, 18, 18, 18, 18, 18, 13, 18, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 18, 18, 18, 18, 18, 18, 18, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 1, 4, 4, 18, 18, 18, 18] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458038742 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742 Building ZINC001458038742 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458038742 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 526) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@]2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1O2) `ZINC001458038742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458038742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001458038742 none CC(C)(C)OC(=O)N1CC[C@]2(C1)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 26, 15, 26, 15, 15, 15, 15, 15, 15, 12, 15, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 15, 15, 15, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 4, 3, 3, 1, 3, 3, 15, 15, 15, 15] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 527) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@]2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1O2) `ZINC001458038742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458038742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001458038742 none CC(C)(C)OC(=O)N1CC[C@]2(C1)C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 30, 18, 30, 18, 18, 18, 18, 18, 18, 13, 18, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 18, 18, 18, 18, 18, 18, 18, 49, 49, 49, 49, 49, 49, 49, 49, 49, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 1, 4, 4, 18, 18, 18, 18] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458038742 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038742 Building ZINC001458038744 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458038744 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/528 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@]2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1O2) `ZINC001458038744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458038744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001458038744 none CC(C)(C)OC(=O)N1CC[C@]2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 17, 31, 17, 17, 17, 17, 17, 17, 10, 17, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 17, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 4, 2, 2, 1, 2, 2, 17, 17, 17, 17] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/529 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@]2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1O2) `ZINC001458038744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458038744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001458038744 none CC(C)(C)OC(=O)N1CC[C@]2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 18, 33, 18, 18, 18, 18, 18, 18, 10, 18, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 18, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18, 4, 2, 2, 1, 2, 2, 18, 18, 18, 18] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458038744 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744 Building ZINC001458038744 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458038744 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 528) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)(C)OC(=O)N1CC[C@]2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1O2) `ZINC001458038744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458038744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001458038744 none CC(C)(C)OC(=O)N1CC[C@]2(C1)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)c1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 17, 31, 17, 17, 17, 17, 17, 17, 10, 17, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 17, 17, 17, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 4, 2, 2, 1, 2, 2, 17, 17, 17, 17] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 529) grep: /scratch/xiaobo/6899/xaj-8058088.10/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)(C)OC(=O)N1CC[C@]2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1O2) `ZINC001458038744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458038744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001458038744 none CC(C)(C)OC(=O)N1CC[C@]2(C1)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)c1ccccc1O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 18, 33, 18, 18, 18, 18, 18, 18, 10, 18, 4, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 18, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18, 4, 2, 2, 1, 2, 2, 18, 18, 18, 18] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458038744 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458038744 Building ZINC001458152074 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458152074 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/530 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458152074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152074 none CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 8, 8, 24, 24, 24, 24, 24, 24, 2, 2, 2, 2, 3, 3, 6, 6, 6, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/531 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458152074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152074 none CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 8, 8, 24, 24, 24, 24, 24, 24, 2, 2, 2, 2, 3, 3, 6, 6, 6, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/532 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/532' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152074.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458152074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152074 none CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 2, 2, 2, 2, 2, 7, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 2, 5, 10, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 7, 7, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2, 5, 5, 10, 10, 10, 5] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 85 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/533 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/533' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152074.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458152074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152074 none CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 2, 2, 2, 2, 2, 7, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 2, 5, 10, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 7, 7, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2, 5, 5, 10, 10, 10, 5] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 85 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458152074 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 Building ZINC001458152074 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458152074 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 530) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458152074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152074 none CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 8, 8, 24, 24, 24, 24, 24, 24, 2, 2, 2, 2, 3, 3, 6, 6, 6, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 531) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458152074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152074 none CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 8, 8, 24, 24, 24, 24, 24, 24, 2, 2, 2, 2, 3, 3, 6, 6, 6, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 532) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152074.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458152074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152074 none CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 2, 2, 2, 2, 2, 7, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 2, 5, 10, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 7, 7, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2, 5, 5, 10, 10, 10, 5] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 85 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 533) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152074.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458152074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152074 none CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 2, 2, 2, 2, 2, 7, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 2, 5, 10, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 7, 7, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2, 5, 5, 10, 10, 10, 5] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 85 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458152074 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 Building ZINC001458152074 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458152074 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 530) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458152074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152074 none CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 8, 8, 24, 24, 24, 24, 24, 24, 2, 2, 2, 2, 3, 3, 6, 6, 6, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 531) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458152074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152074 none CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 8, 8, 24, 24, 24, 24, 24, 24, 2, 2, 2, 2, 3, 3, 6, 6, 6, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 532) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152074.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458152074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152074 none CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 2, 2, 2, 2, 2, 7, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 2, 5, 10, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 7, 7, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2, 5, 5, 10, 10, 10, 5] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 85 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 533) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152074.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458152074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152074 none CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 2, 2, 2, 2, 2, 7, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 2, 5, 10, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 7, 7, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2, 5, 5, 10, 10, 10, 5] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 85 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458152074 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 Building ZINC001458152074 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458152074 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 530) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458152074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152074 none CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 8, 8, 24, 24, 24, 24, 24, 24, 2, 2, 2, 2, 3, 3, 6, 6, 6, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 531) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458152074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152074 none CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 24, 24, 24, 24, 24, 24, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 8, 8, 24, 24, 24, 24, 24, 24, 2, 2, 2, 2, 3, 3, 6, 6, 6, 3] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 532) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152074.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458152074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152074 none CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 2, 2, 2, 2, 2, 7, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 2, 5, 10, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 7, 7, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2, 5, 5, 10, 10, 10, 5] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 85 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 533) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152074.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458152074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152074 none CC[C@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 2, 2, 2, 2, 2, 7, 21, 21, 21, 21, 21, 21, 2, 2, 2, 1, 2, 1, 1, 1, 5, 5, 2, 5, 10, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 7, 7, 21, 21, 21, 21, 21, 21, 2, 2, 2, 2, 5, 5, 10, 10, 10, 5] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 85 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458152074 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152074 Building ZINC001458152083 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458152083 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/534 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458152083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152083 none CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 4, 5, 5, 4, 4, 4, 4, 4, 10, 25, 25, 25, 25, 25, 25, 4, 4, 4, 2, 4, 1, 1, 1, 3, 3, 2, 3, 5, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 10, 10, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 3, 3, 5, 5, 5, 3] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 77 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/535 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458152083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152083 none CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 4, 5, 5, 4, 4, 4, 4, 4, 10, 25, 25, 25, 25, 25, 25, 4, 4, 4, 2, 4, 1, 1, 1, 3, 3, 2, 3, 5, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 10, 10, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 3, 3, 5, 5, 5, 3] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 77 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/536 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/536' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152083.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458152083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152083 none CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need 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, 3, 4, 4, 3, 3, 3, 3, 3, 9, 25, 25, 25, 25, 25, 25, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 9, 9, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3, 2, 2, 4, 4, 4, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/537 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/537' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152083.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458152083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152083 none CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need 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, 3, 4, 4, 3, 3, 3, 3, 3, 9, 25, 25, 25, 25, 25, 25, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 9, 9, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3, 2, 2, 4, 4, 4, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458152083 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 Building ZINC001458152083 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458152083 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 534) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458152083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152083 none CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 4, 5, 5, 4, 4, 4, 4, 4, 10, 25, 25, 25, 25, 25, 25, 4, 4, 4, 2, 4, 1, 1, 1, 3, 3, 2, 3, 5, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 10, 10, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 3, 3, 5, 5, 5, 3] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 77 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 535) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458152083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152083 none CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 4, 5, 5, 4, 4, 4, 4, 4, 10, 25, 25, 25, 25, 25, 25, 4, 4, 4, 2, 4, 1, 1, 1, 3, 3, 2, 3, 5, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 10, 10, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 3, 3, 5, 5, 5, 3] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 77 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 536) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152083.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458152083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152083 none CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need 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, 3, 4, 4, 3, 3, 3, 3, 3, 9, 25, 25, 25, 25, 25, 25, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 9, 9, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3, 2, 2, 4, 4, 4, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 537) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152083.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458152083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152083 none CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need 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, 3, 4, 4, 3, 3, 3, 3, 3, 9, 25, 25, 25, 25, 25, 25, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 9, 9, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3, 2, 2, 4, 4, 4, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458152083 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 Building ZINC001458152083 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458152083 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 534) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458152083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152083 none CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 4, 5, 5, 4, 4, 4, 4, 4, 10, 25, 25, 25, 25, 25, 25, 4, 4, 4, 2, 4, 1, 1, 1, 3, 3, 2, 3, 5, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 10, 10, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 3, 3, 5, 5, 5, 3] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 77 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 535) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458152083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152083 none CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 4, 5, 5, 4, 4, 4, 4, 4, 10, 25, 25, 25, 25, 25, 25, 4, 4, 4, 2, 4, 1, 1, 1, 3, 3, 2, 3, 5, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 10, 10, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 3, 3, 5, 5, 5, 3] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 77 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 536) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152083.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458152083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152083 none CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need 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, 3, 4, 4, 3, 3, 3, 3, 3, 9, 25, 25, 25, 25, 25, 25, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 9, 9, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3, 2, 2, 4, 4, 4, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 537) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152083.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458152083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152083 none CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need 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, 3, 4, 4, 3, 3, 3, 3, 3, 9, 25, 25, 25, 25, 25, 25, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 9, 9, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3, 2, 2, 4, 4, 4, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458152083 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 Building ZINC001458152083 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458152083 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 534) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458152083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152083 none CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 4, 5, 5, 4, 4, 4, 4, 4, 10, 25, 25, 25, 25, 25, 25, 4, 4, 4, 2, 4, 1, 1, 1, 3, 3, 2, 3, 5, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 10, 10, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 3, 3, 5, 5, 5, 3] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 77 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 535) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458152083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152083 none CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 4, 5, 5, 4, 4, 4, 4, 4, 10, 25, 25, 25, 25, 25, 25, 4, 4, 4, 2, 4, 1, 1, 1, 3, 3, 2, 3, 5, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 10, 10, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 3, 3, 5, 5, 5, 3] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 77 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 536) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152083.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458152083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152083 none CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need 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, 3, 4, 4, 3, 3, 3, 3, 3, 9, 25, 25, 25, 25, 25, 25, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 9, 9, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3, 2, 2, 4, 4, 4, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 537) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152083.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458152083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152083 none CC[C@@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need 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, 3, 4, 4, 3, 3, 3, 3, 3, 9, 25, 25, 25, 25, 25, 25, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 9, 9, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3, 2, 2, 4, 4, 4, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458152083 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152083 Building ZINC001458152092 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458152092 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/538 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458152092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152092 none CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 8, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/539 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458152092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152092 none CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 8, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/540 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/540' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152092.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458152092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152092 none CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 7, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 7, 7, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/541 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/541' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152092.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458152092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152092 none CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 7, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 7, 7, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458152092 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 Building ZINC001458152092 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458152092 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 538) grep: /scratch/xiaobo/6899/xaj-8058088.10/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@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458152092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152092 none CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 8, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 539) grep: /scratch/xiaobo/6899/xaj-8058088.10/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@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458152092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152092 none CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 8, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 540) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152092.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458152092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152092 none CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 7, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 7, 7, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 541) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152092.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458152092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152092 none CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 7, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 7, 7, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458152092 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 Building ZINC001458152092 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458152092 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 538) grep: /scratch/xiaobo/6899/xaj-8058088.10/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@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458152092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152092 none CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 8, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 539) grep: /scratch/xiaobo/6899/xaj-8058088.10/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@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458152092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152092 none CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 8, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 540) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152092.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458152092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152092 none CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 7, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 7, 7, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 541) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152092.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458152092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152092 none CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 7, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 7, 7, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458152092 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 Building ZINC001458152092 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458152092 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 538) grep: /scratch/xiaobo/6899/xaj-8058088.10/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@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458152092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152092 none CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 8, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 539) grep: /scratch/xiaobo/6899/xaj-8058088.10/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@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458152092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152092 none CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 8, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 540) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152092.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458152092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152092 none CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 7, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 7, 7, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 541) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152092.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458152092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152092 none CC[C@@H](C)[C@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 7, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 7, 7, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458152092 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152092 Building ZINC001458152098 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458152098 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/542 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458152098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152098 none CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 3, 4, 4, 3, 3, 3, 3, 3, 9, 23, 23, 23, 23, 23, 23, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 5, 5, 5, 5, 5, 4, 4, 4, 3, 3, 9, 9, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 74 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/543 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458152098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152098 none CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 3, 4, 4, 3, 3, 3, 3, 3, 9, 23, 23, 23, 23, 23, 23, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 5, 5, 5, 5, 5, 4, 4, 4, 3, 3, 9, 9, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 74 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/544 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/544' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152098.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458152098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152098 none CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 8, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/545 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/545' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152098.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458152098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152098 none CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 8, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458152098 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 Building ZINC001458152098 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458152098 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 542) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458152098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152098 none CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 3, 4, 4, 3, 3, 3, 3, 3, 9, 23, 23, 23, 23, 23, 23, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 5, 5, 5, 5, 5, 4, 4, 4, 3, 3, 9, 9, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 74 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 543) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458152098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152098 none CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 3, 4, 4, 3, 3, 3, 3, 3, 9, 23, 23, 23, 23, 23, 23, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 5, 5, 5, 5, 5, 4, 4, 4, 3, 3, 9, 9, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 74 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 544) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152098.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458152098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152098 none CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 8, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 545) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152098.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458152098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152098 none CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 8, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458152098 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 Building ZINC001458152098 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458152098 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 542) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458152098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152098 none CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 3, 4, 4, 3, 3, 3, 3, 3, 9, 23, 23, 23, 23, 23, 23, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 5, 5, 5, 5, 5, 4, 4, 4, 3, 3, 9, 9, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 74 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 543) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458152098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152098 none CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 3, 4, 4, 3, 3, 3, 3, 3, 9, 23, 23, 23, 23, 23, 23, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 5, 5, 5, 5, 5, 4, 4, 4, 3, 3, 9, 9, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 74 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 544) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152098.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458152098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152098 none CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 8, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 545) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152098.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458152098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152098 none CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 8, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458152098 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 Building ZINC001458152098 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458152098 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 542) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458152098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152098 none CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 3, 4, 4, 3, 3, 3, 3, 3, 9, 23, 23, 23, 23, 23, 23, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 5, 5, 5, 5, 5, 4, 4, 4, 3, 3, 9, 9, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 74 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 543) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458152098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152098 none CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 3, 4, 4, 3, 3, 3, 3, 3, 9, 23, 23, 23, 23, 23, 23, 3, 3, 3, 2, 3, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 5, 5, 5, 5, 5, 4, 4, 4, 3, 3, 9, 9, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 74 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 544) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152098.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458152098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152098 none CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 8, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 545) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC001458152098.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458152098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001458152098 none CC[C@H](C)[C@@H]1CN(Cc2ccc(C)nc2)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 10, 5, 1, 1, 1, 1, 5, 8, 1, 5, 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, 7, 7, 7, 7, 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, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 3, 2, 2, 2, 2, 2, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 4, 4, 4, 4, 4, 3, 3, 3, 2, 2, 8, 8, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 5, 5, 5, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458152098 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458152098 Building ZINC001458212153 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458212153 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/546 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(C(F)(F)F)cc3)CC2)cc1Cl) `ZINC001458212153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458212153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001458212153 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(C(F)(F)F)cc3)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', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 9, 15, 15, 15, 15, 25, 25, 24, 24, 25, 25, 25, 25, 25, 15, 15, 4, 4, 4, 8, 8, 8, 4, 4, 15, 15, 15, 15, 25, 25, 25, 25, 15, 15, 15, 15, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/547 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(C(F)(F)F)cc3)CC2)cc1Cl) `ZINC001458212153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458212153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001458212153 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(C(F)(F)F)cc3)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', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 4, 9, 15, 15, 15, 15, 26, 26, 23, 23, 26, 26, 26, 26, 26, 15, 15, 2, 2, 2, 5, 5, 5, 2, 2, 15, 15, 15, 15, 26, 26, 26, 26, 15, 15, 15, 15, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458212153 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153 Building ZINC001458212153 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458212153 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 546) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(C(F)(F)F)cc3)CC2)cc1Cl) `ZINC001458212153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458212153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001458212153 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(C(F)(F)F)cc3)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', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 9, 15, 15, 15, 15, 25, 25, 24, 24, 25, 25, 25, 25, 25, 15, 15, 4, 4, 4, 8, 8, 8, 4, 4, 15, 15, 15, 15, 25, 25, 25, 25, 15, 15, 15, 15, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 547) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(C(F)(F)F)cc3)CC2)cc1Cl) `ZINC001458212153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458212153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001458212153 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(C(F)(F)F)cc3)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', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 2, 1, 1, 1, 1, 4, 9, 15, 15, 15, 15, 26, 26, 23, 23, 26, 26, 26, 26, 26, 15, 15, 2, 2, 2, 5, 5, 5, 2, 2, 15, 15, 15, 15, 26, 26, 26, 26, 15, 15, 15, 15, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458212153 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458212153 Building ZINC001458432024 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458432024 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/548 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458432024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432024 none CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 6, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 4, 10, 10, 10, 10, 10, 10, 2, 2, 8, 8, 8, 8, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 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, 53, 54, 55, 56, 57]) total number of confs: 62 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/549 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458432024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432024 none CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 6, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 4, 10, 10, 10, 10, 10, 10, 2, 2, 8, 8, 8, 8, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 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, 53, 54, 55, 56, 57]) total number of confs: 62 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/550 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/550' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432024.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458432024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432024 none CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 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, 53, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/551 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/551' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432024.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458432024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432024 none CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 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, 53, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458432024 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 Building ZINC001458432024 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458432024 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 548) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458432024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432024 none CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 6, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 4, 10, 10, 10, 10, 10, 10, 2, 2, 8, 8, 8, 8, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 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, 53, 54, 55, 56, 57]) total number of confs: 62 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 549) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458432024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432024 none CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 6, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 4, 10, 10, 10, 10, 10, 10, 2, 2, 8, 8, 8, 8, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 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, 53, 54, 55, 56, 57]) total number of confs: 62 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 550) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432024.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458432024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432024 none CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 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, 53, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 551) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432024.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458432024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432024 none CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 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, 53, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458432024 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 Building ZINC001458432024 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458432024 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 548) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458432024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432024 none CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 6, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 4, 10, 10, 10, 10, 10, 10, 2, 2, 8, 8, 8, 8, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 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, 53, 54, 55, 56, 57]) total number of confs: 62 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 549) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458432024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432024 none CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 6, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 4, 10, 10, 10, 10, 10, 10, 2, 2, 8, 8, 8, 8, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 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, 53, 54, 55, 56, 57]) total number of confs: 62 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 550) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432024.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458432024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432024 none CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 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, 53, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 551) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432024.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458432024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432024 none CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 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, 53, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458432024 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 Building ZINC001458432024 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458432024 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 548) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458432024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432024 none CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 6, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 4, 10, 10, 10, 10, 10, 10, 2, 2, 8, 8, 8, 8, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 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, 53, 54, 55, 56, 57]) total number of confs: 62 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 549) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458432024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432024 none CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 6, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 4, 10, 10, 10, 10, 10, 10, 2, 2, 8, 8, 8, 8, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 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, 53, 54, 55, 56, 57]) total number of confs: 62 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 550) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432024.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458432024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432024 none CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 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, 53, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 551) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432024.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458432024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432024 none CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 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, 53, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458432024 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432024 Building ZINC001458432025 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458432025 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/552 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458432025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432025 none CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 4, 3, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/553 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458432025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432025 none CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 4, 3, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/554 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/554' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432025.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458432025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432025 none CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 5, 3, 6, 1, 1, 1, 2, 2, 2, 2, 2, 16, 16, 3, 16, 16, 16, 16, 16, 16, 2, 2, 6, 6, 6, 6, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 2, 2, 2, 16, 16, 4, 16, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 58 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/555 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/555' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432025.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458432025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432025 none CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 5, 3, 6, 1, 1, 1, 2, 2, 2, 2, 2, 16, 16, 3, 16, 16, 16, 16, 16, 16, 2, 2, 6, 6, 6, 6, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 2, 2, 2, 16, 16, 4, 16, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 58 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458432025 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 Building ZINC001458432025 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458432025 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 552) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458432025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432025 none CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 4, 3, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 553) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458432025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432025 none CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 4, 3, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 554) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432025.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458432025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432025 none CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 5, 3, 6, 1, 1, 1, 2, 2, 2, 2, 2, 16, 16, 3, 16, 16, 16, 16, 16, 16, 2, 2, 6, 6, 6, 6, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 2, 2, 2, 16, 16, 4, 16, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 58 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 555) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432025.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458432025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432025 none CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 5, 3, 6, 1, 1, 1, 2, 2, 2, 2, 2, 16, 16, 3, 16, 16, 16, 16, 16, 16, 2, 2, 6, 6, 6, 6, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 2, 2, 2, 16, 16, 4, 16, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 58 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458432025 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 Building ZINC001458432025 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458432025 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 552) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458432025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432025 none CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 4, 3, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 553) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458432025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432025 none CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 4, 3, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 554) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432025.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458432025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432025 none CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 5, 3, 6, 1, 1, 1, 2, 2, 2, 2, 2, 16, 16, 3, 16, 16, 16, 16, 16, 16, 2, 2, 6, 6, 6, 6, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 2, 2, 2, 16, 16, 4, 16, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 58 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 555) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432025.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458432025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432025 none CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 5, 3, 6, 1, 1, 1, 2, 2, 2, 2, 2, 16, 16, 3, 16, 16, 16, 16, 16, 16, 2, 2, 6, 6, 6, 6, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 2, 2, 2, 16, 16, 4, 16, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 58 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458432025 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 Building ZINC001458432025 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458432025 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 552) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458432025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432025 none CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 4, 3, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 553) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458432025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432025 none CCN1C[C@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 4, 3, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 554) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432025.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458432025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432025 none CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 5, 3, 6, 1, 1, 1, 2, 2, 2, 2, 2, 16, 16, 3, 16, 16, 16, 16, 16, 16, 2, 2, 6, 6, 6, 6, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 2, 2, 2, 16, 16, 4, 16, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 58 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 555) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432025.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458432025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432025 none CCN1C[C@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 5, 3, 6, 1, 1, 1, 2, 2, 2, 2, 2, 16, 16, 3, 16, 16, 16, 16, 16, 16, 2, 2, 6, 6, 6, 6, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 2, 2, 2, 16, 16, 4, 16, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 58 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458432025 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432025 Building ZINC001458432026 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458432026 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/556 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458432026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432026 none CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 4, 5, 1, 1, 1, 2, 2, 2, 2, 2, 19, 19, 3, 19, 19, 19, 19, 19, 19, 2, 2, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 2, 2, 2, 19, 19, 4, 19, 2, 2, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/557 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458432026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432026 none CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 4, 5, 1, 1, 1, 2, 2, 2, 2, 2, 19, 19, 3, 19, 19, 19, 19, 19, 19, 2, 2, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 2, 2, 2, 19, 19, 4, 19, 2, 2, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/558 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/558' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432026.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458432026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432026 none CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 5, 4, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 3, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/559 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/559' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432026.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458432026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432026 none CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 5, 4, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 3, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458432026 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 Building ZINC001458432026 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458432026 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 556) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458432026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432026 none CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 4, 5, 1, 1, 1, 2, 2, 2, 2, 2, 19, 19, 3, 19, 19, 19, 19, 19, 19, 2, 2, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 2, 2, 2, 19, 19, 4, 19, 2, 2, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 557) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458432026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432026 none CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 4, 5, 1, 1, 1, 2, 2, 2, 2, 2, 19, 19, 3, 19, 19, 19, 19, 19, 19, 2, 2, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 2, 2, 2, 19, 19, 4, 19, 2, 2, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 558) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432026.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458432026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432026 none CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 5, 4, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 3, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 559) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432026.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458432026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432026 none CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 5, 4, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 3, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458432026 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 Building ZINC001458432026 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458432026 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 556) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458432026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432026 none CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 4, 5, 1, 1, 1, 2, 2, 2, 2, 2, 19, 19, 3, 19, 19, 19, 19, 19, 19, 2, 2, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 2, 2, 2, 19, 19, 4, 19, 2, 2, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 557) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458432026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432026 none CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 4, 5, 1, 1, 1, 2, 2, 2, 2, 2, 19, 19, 3, 19, 19, 19, 19, 19, 19, 2, 2, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 2, 2, 2, 19, 19, 4, 19, 2, 2, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 558) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432026.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458432026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432026 none CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 5, 4, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 3, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 559) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432026.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458432026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432026 none CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 5, 4, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 3, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458432026 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 Building ZINC001458432026 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458432026 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 556) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458432026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432026 none CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 4, 5, 1, 1, 1, 2, 2, 2, 2, 2, 19, 19, 3, 19, 19, 19, 19, 19, 19, 2, 2, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 2, 2, 2, 19, 19, 4, 19, 2, 2, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 557) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458432026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432026 none CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 4, 5, 1, 1, 1, 2, 2, 2, 2, 2, 19, 19, 3, 19, 19, 19, 19, 19, 19, 2, 2, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 2, 2, 2, 19, 19, 4, 19, 2, 2, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 558) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432026.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458432026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432026 none CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 5, 4, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 3, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 559) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C) `ZINC001458432026.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458432026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432026 none CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 5, 4, 5, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 3, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458432026 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432026 Building ZINC001458432027 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458432027 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/560 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458432027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432027 none CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 63 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/561 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458432027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432027 none CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 63 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/562 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/562' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432027.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458432027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432027 none CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/563 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/563' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432027.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458432027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432027 none CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458432027 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 Building ZINC001458432027 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458432027 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 560) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458432027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432027 none CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 63 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 561) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458432027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432027 none CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 63 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 562) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432027.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458432027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432027 none CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 563) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432027.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458432027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432027 none CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458432027 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 Building ZINC001458432027 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458432027 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 560) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458432027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432027 none CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 63 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 561) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458432027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432027 none CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 63 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 562) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432027.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458432027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432027 none CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 563) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432027.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458432027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432027 none CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458432027 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 Building ZINC001458432027 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458432027 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 560) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458432027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432027 none CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 63 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 561) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458432027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432027 none CCN1C[C@@H](C)N(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 4, 12, 12, 12, 12, 12, 12, 2, 2, 6, 6, 6, 6, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 63 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 562) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432027.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458432027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432027 none CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 563) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C) `ZINC001458432027.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458432027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001458432027 none CCN1C[C@@H](C)N(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 7, 7, 4, 2, 6, 1, 1, 1, 3, 3, 3, 3, 3, 15, 15, 3, 15, 15, 15, 15, 15, 15, 3, 3, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 3, 3, 3, 15, 15, 3, 15, 3, 3, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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, 53, 54, 55, 56, 57]) total number of confs: 67 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458432027 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458432027 Building ZINC001458532107 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458532107 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/564 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1OC) `ZINC001458532107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458532107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001458532107 none COc1ccc(C[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 30, 30, 30, 30, 22, 21, 12, 21, 21, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 30, 30, 30, 45, 48, 48, 48, 30, 30, 22, 22, 21, 21, 21, 12, 12, 3, 4, 4, 30, 45, 45, 45] 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: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/565 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1OC) `ZINC001458532107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458532107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001458532107 none COc1ccc(C[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 29, 18, 16, 9, 16, 16, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 29, 29, 29, 48, 50, 50, 50, 29, 29, 18, 18, 16, 16, 16, 9, 9, 2, 3, 3, 29, 48, 48, 48] 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: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458532107 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107 Building ZINC001458532107 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458532107 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 564) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1OC) `ZINC001458532107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458532107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001458532107 none COc1ccc(C[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 30, 30, 30, 30, 22, 21, 12, 21, 21, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 30, 30, 30, 45, 48, 48, 48, 30, 30, 22, 22, 21, 21, 21, 12, 12, 3, 4, 4, 30, 45, 45, 45] 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: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 565) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1OC) `ZINC001458532107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458532107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001458532107 none COc1ccc(C[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 29, 18, 16, 9, 16, 16, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 29, 29, 29, 48, 50, 50, 50, 29, 29, 18, 18, 16, 16, 16, 9, 9, 2, 3, 3, 29, 48, 48, 48] 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: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458532107 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532107 Building ZINC001458532110 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458532110 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/566 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1OC) `ZINC001458532110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458532110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001458532110 none COc1ccc(C[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 29, 18, 16, 9, 16, 16, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 29, 29, 29, 47, 49, 49, 49, 29, 29, 18, 18, 16, 16, 16, 9, 9, 2, 4, 4, 29, 47, 47, 47] 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/567 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C[C@H](C)CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1OC) `ZINC001458532110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458532110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001458532110 none COc1ccc(C[C@H](C)CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 21, 20, 12, 20, 20, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 31, 31, 31, 46, 48, 48, 48, 31, 31, 21, 21, 20, 20, 20, 12, 12, 3, 3, 3, 31, 46, 46, 46] 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: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458532110 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110 Building ZINC001458532110 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458532110 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 566) grep: /scratch/xiaobo/6899/xaj-8058088.10/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[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1OC) `ZINC001458532110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458532110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001458532110 none COc1ccc(C[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 29, 18, 16, 9, 16, 16, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 29, 29, 29, 47, 49, 49, 49, 29, 29, 18, 18, 16, 16, 16, 9, 9, 2, 4, 4, 29, 47, 47, 47] 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: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 567) grep: /scratch/xiaobo/6899/xaj-8058088.10/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[C@H](C)CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1OC) `ZINC001458532110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458532110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001458532110 none COc1ccc(C[C@H](C)CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 31, 31, 31, 21, 20, 12, 20, 20, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 31, 31, 31, 46, 48, 48, 48, 31, 31, 21, 21, 20, 20, 20, 12, 12, 3, 3, 3, 31, 46, 46, 46] 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: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458532110 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458532110 Building ZINC001458538676 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458538676 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/568 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(Br)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001458538676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458538676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001458538676 none C[N@]1CC[N@](c2ccc(Br)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 10, 10, 5, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/569 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(Br)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001458538676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458538676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001458538676 none C[N@]1CC[N@@](c2ccc(Br)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 14, 9, 9, 6, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/570 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/570' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(Br)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001458538676.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458538676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001458538676 none C[N@]1CC[N@](c2ccc(Br)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 10, 10, 7, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/571 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/571' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(Br)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001458538676.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458538676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001458538676 none C[N@]1CC[N@@](c2ccc(Br)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 14, 9, 9, 4, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458538676 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 Building ZINC001458538676 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458538676 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 568) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(Br)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001458538676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458538676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001458538676 none C[N@]1CC[N@](c2ccc(Br)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 10, 10, 5, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 569) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(Br)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001458538676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458538676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001458538676 none C[N@]1CC[N@@](c2ccc(Br)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 14, 9, 9, 6, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 570) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(Br)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001458538676.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458538676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001458538676 none C[N@]1CC[N@](c2ccc(Br)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 10, 10, 7, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 571) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(Br)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001458538676.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458538676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001458538676 none C[N@]1CC[N@@](c2ccc(Br)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 14, 9, 9, 4, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458538676 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 Building ZINC001458538676 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458538676 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 568) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(Br)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001458538676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458538676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001458538676 none C[N@]1CC[N@](c2ccc(Br)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 10, 10, 5, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 569) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(Br)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001458538676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458538676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001458538676 none C[N@]1CC[N@@](c2ccc(Br)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 14, 9, 9, 6, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 570) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(Br)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001458538676.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458538676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001458538676 none C[N@]1CC[N@](c2ccc(Br)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 10, 10, 7, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 571) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(Br)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001458538676.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458538676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001458538676 none C[N@]1CC[N@@](c2ccc(Br)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 14, 9, 9, 4, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458538676 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 Building ZINC001458538676 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001458538676 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 568) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(Br)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001458538676.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458538676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001458538676 none C[N@]1CC[N@](c2ccc(Br)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 10, 10, 5, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 569) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(Br)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001458538676.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458538676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001458538676 none C[N@]1CC[N@@](c2ccc(Br)cc2NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 14, 9, 9, 6, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 570) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(Br)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001458538676.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001458538676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001458538676 none C[N@]1CC[N@](c2ccc(Br)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 10, 10, 7, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 571) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(Br)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC001458538676.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001458538676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001458538676 none C[N@]1CC[N@@](c2ccc(Br)cc2NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 14, 9, 9, 4, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458538676 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458538676 Building ZINC001458845858 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458845858 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/572 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](n2ccc(C(F)(F)F)n2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458845858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458845858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001458845858 none O=C(N1CCC[C@@H](n2ccc(C(F)(F)F)n2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 5, 15, 15, 15, 8, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 10, 10, 10, 10, 10, 10, 36, 36, 36, 36, 36, 36, 36, 36, 10, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 36, 36, 10, 10, 2, 2] 50 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/573 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/573' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](n2ccc(C(F)(F)F)n2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458845858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458845858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001458845858 none O=C(N1CCC[C@@H](n2ccc(C(F)(F)F)n2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 5, 15, 15, 15, 8, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 32, 32, 32, 11, 1, 1, 1, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 32, 32, 11, 11, 3, 3] 50 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458845858 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858 Building ZINC001458845858 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458845858 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 572) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](n2ccc(C(F)(F)F)n2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458845858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458845858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001458845858 none O=C(N1CCC[C@@H](n2ccc(C(F)(F)F)n2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 5, 15, 15, 15, 8, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 10, 10, 10, 10, 10, 10, 36, 36, 36, 36, 36, 36, 36, 36, 10, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 36, 36, 10, 10, 2, 2] 50 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 573) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](n2ccc(C(F)(F)F)n2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458845858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458845858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001458845858 none O=C(N1CCC[C@@H](n2ccc(C(F)(F)F)n2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 5, 15, 15, 15, 8, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 32, 32, 32, 32, 32, 32, 32, 11, 1, 1, 1, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 32, 32, 11, 11, 3, 3] 50 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458845858 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845858 Building ZINC001458845864 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458845864 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/574 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](n2ccc(C(F)(F)F)n2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458845864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458845864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001458845864 none O=C(N1CCC[C@H](n2ccc(C(F)(F)F)n2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 5, 15, 15, 15, 8, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 36, 36, 36, 36, 36, 36, 36, 36, 11, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 36, 36, 11, 11, 5, 5] 50 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/575 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](n2ccc(C(F)(F)F)n2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458845864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458845864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001458845864 none O=C(N1CCC[C@H](n2ccc(C(F)(F)F)n2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 5, 15, 15, 15, 8, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 13, 13, 13, 40, 40, 40, 40, 40, 40, 40, 40, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 40, 40, 13, 13, 3, 3] 50 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458845864 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864 Building ZINC001458845864 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001458845864 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 574) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(N1CCC[C@H](n2ccc(C(F)(F)F)n2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458845864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001458845864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001458845864 none O=C(N1CCC[C@H](n2ccc(C(F)(F)F)n2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 5, 15, 15, 15, 8, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 11, 11, 11, 36, 36, 36, 36, 36, 36, 36, 36, 11, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 36, 36, 11, 11, 5, 5] 50 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 575) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(N1CCC[C@H](n2ccc(C(F)(F)F)n2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001458845864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001458845864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001458845864 none O=C(N1CCC[C@H](n2ccc(C(F)(F)F)n2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 8, 1, 1, 1, 5, 15, 15, 15, 8, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 13, 13, 13, 13, 40, 40, 40, 40, 40, 40, 40, 40, 13, 1, 1, 1, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 40, 40, 13, 13, 3, 3] 50 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001458845864 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001458845864 Building ZINC001459044694 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459044694 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/576 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1) `ZINC001459044694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459044694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001459044694 none C[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', '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', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 17, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 25, 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, 49, 50, 51]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/577 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1) `ZINC001459044694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459044694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001459044694 none C[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', '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', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 17, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 25, 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, 49, 50, 51]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/578 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/578' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1) `ZINC001459044694.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459044694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001459044694 none C[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', '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', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 17, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 26, 26, 26, 26] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/579 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/579' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1) `ZINC001459044694.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459044694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001459044694 none C[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', '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', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 17, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 26, 26, 26, 26] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459044694 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 Building ZINC001459044694 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459044694 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 576) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1) `ZINC001459044694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459044694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001459044694 none C[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', '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', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 17, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 25, 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, 49, 50, 51]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 577) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1) `ZINC001459044694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459044694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001459044694 none C[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', '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', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 17, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 25, 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, 49, 50, 51]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 578) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1) `ZINC001459044694.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459044694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001459044694 none C[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', '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', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 17, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 26, 26, 26, 26] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 579) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1) `ZINC001459044694.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459044694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001459044694 none C[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', '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', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 17, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 26, 26, 26, 26] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459044694 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 Building ZINC001459044694 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459044694 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 576) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1) `ZINC001459044694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459044694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001459044694 none C[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', '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', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 17, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 25, 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, 49, 50, 51]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 577) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1) `ZINC001459044694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459044694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001459044694 none C[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', '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', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 17, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 25, 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, 49, 50, 51]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 578) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1) `ZINC001459044694.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459044694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001459044694 none C[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', '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', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 17, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 26, 26, 26, 26] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 579) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1) `ZINC001459044694.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459044694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001459044694 none C[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', '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', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 17, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 26, 26, 26, 26] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459044694 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 Building ZINC001459044694 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459044694 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 576) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1) `ZINC001459044694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459044694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001459044694 none C[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', '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', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 17, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 25, 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, 49, 50, 51]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 577) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1) `ZINC001459044694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459044694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001459044694 none C[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', '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', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 17, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 25, 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, 49, 50, 51]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 578) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1) `ZINC001459044694.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459044694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001459044694 none C[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', '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', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 17, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 26, 26, 26, 26] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 579) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1) `ZINC001459044694.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459044694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001459044694 none C[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2Br)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', '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', 'Br', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 17, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 8, 12, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 26, 26, 26, 26] 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: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459044694 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459044694 Building ZINC001459293360 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459293360 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/580 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/580' -> `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)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001459293360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459293360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001459293360 none C[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', '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', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 20, 20, 31, 31, 31, 31, 10, 10, 10, 10, 7, 1, 9, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 10, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/581 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/581' -> `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)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001459293360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459293360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001459293360 none C[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', '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', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 31, 31, 31, 31, 11, 11, 11, 11, 8, 1, 9, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 11, 11, 11, 11, 11, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459293360 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360 Building ZINC001459293360 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459293360 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 580) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001459293360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459293360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001459293360 none C[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H](C)N1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', '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', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 20, 20, 31, 31, 31, 31, 10, 10, 10, 10, 7, 1, 9, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 10, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 581) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001459293360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459293360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001459293360 none C[C@@H]1CN(C(=O)OC(C)(C)C)C[C@H](C)N1C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 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', 'H', 'C.3', 'N.am', 'C.2', 'O.2', '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', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 31, 31, 31, 31, 11, 11, 11, 11, 8, 1, 9, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 11, 11, 11, 11, 11, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459293360 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459293360 Building ZINC001459466479 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459466479 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/582 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H](c2cccc(F)c2)C1) `ZINC001459466479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459466479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001459466479 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H](c2cccc(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 3, 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, 24, 24, 24, 11, 6, 11, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 14, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 1, 1, 1, 1, 14, 14, 14, 14, 6, 6] 50 rigid atoms, others: [48, 45, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] 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, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53, 54]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/583 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/583' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H](c2cccc(F)c2)C1) `ZINC001459466479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459466479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001459466479 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H](c2cccc(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 3, 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, 23, 24, 24, 14, 8, 14, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 23, 23, 23, 23, 23, 23, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 1, 1, 1, 1, 23, 23, 23, 23, 8, 8] 50 rigid atoms, others: [48, 45, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] 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, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53, 54]) total number of confs: 82 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459466479 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479 Building ZINC001459466479 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459466479 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 582) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H](c2cccc(F)c2)C1) `ZINC001459466479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459466479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001459466479 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@H](c2cccc(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 3, 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, 24, 24, 24, 11, 6, 11, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 14, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 1, 1, 1, 1, 14, 14, 14, 14, 6, 6] 50 rigid atoms, others: [48, 45, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] 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, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53, 54]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 583) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H](c2cccc(F)c2)C1) `ZINC001459466479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459466479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001459466479 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@H](c2cccc(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 3, 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, 23, 24, 24, 14, 8, 14, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 23, 23, 23, 23, 23, 23, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 1, 1, 1, 1, 23, 23, 23, 23, 8, 8] 50 rigid atoms, others: [48, 45, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] 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, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53, 54]) total number of confs: 82 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459466479 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466479 Building ZINC001459466481 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459466481 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/584 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](c2cccc(F)c2)C1) `ZINC001459466481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459466481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001459466481 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](c2cccc(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 3, 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, 24, 24, 24, 15, 8, 15, 8, 8, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 26, 26, 26, 26, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 1, 1, 1, 1, 26, 26, 26, 26, 8, 8] 50 rigid atoms, others: [48, 45, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] 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, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53, 54]) total number of confs: 87 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/585 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/585' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](c2cccc(F)c2)C1) `ZINC001459466481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459466481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001459466481 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](c2cccc(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 3, 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, 22, 22, 22, 11, 6, 11, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 14, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 1, 1, 1, 1, 14, 14, 14, 14, 6, 6] 50 rigid atoms, others: [48, 45, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] 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, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53, 54]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459466481 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481 Building ZINC001459466481 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459466481 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 584) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](c2cccc(F)c2)C1) `ZINC001459466481.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459466481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001459466481 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](c2cccc(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 3, 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, 24, 24, 24, 15, 8, 15, 8, 8, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 26, 26, 26, 26, 26, 26, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 1, 1, 1, 1, 26, 26, 26, 26, 8, 8] 50 rigid atoms, others: [48, 45, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] 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, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53, 54]) total number of confs: 87 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 585) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](c2cccc(F)c2)C1) `ZINC001459466481.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459466481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001459466481 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)[C@@H](c2cccc(F)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 1, 1, 1, 1, 1, 15, 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, 7, 7, 7, 3, 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, 22, 22, 22, 11, 6, 11, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 14, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 1, 1, 1, 1, 14, 14, 14, 14, 6, 6] 50 rigid atoms, others: [48, 45, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] 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, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53, 54]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459466481 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459466481 Building ZINC001459613119 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459613119 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/586 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCc1ccccn1)Cc1ccncc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001459613119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459613119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001459613119 none O=C(N(CCc1ccccn1)Cc1ccncc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens need 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, 6, 10, 10, 17, 17, 17, 17, 17, 6, 14, 18, 18, 17, 18, 18, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 10, 17, 17, 17, 17, 14, 14, 18, 18, 18, 18, 4, 4] 50 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/587 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/587' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCc1ccccn1)Cc1ccncc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001459613119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459613119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001459613119 none O=C(N(CCc1ccccn1)Cc1ccncc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens need 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, 6, 10, 10, 19, 19, 19, 19, 19, 6, 15, 19, 19, 18, 19, 19, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 10, 19, 19, 19, 19, 15, 15, 19, 19, 19, 19, 4, 4] 50 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: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459613119 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119 Building ZINC001459613119 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459613119 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 586) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N(CCc1ccccn1)Cc1ccncc1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001459613119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459613119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001459613119 none O=C(N(CCc1ccccn1)Cc1ccncc1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens need 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, 6, 10, 10, 17, 17, 17, 17, 17, 6, 14, 18, 18, 17, 18, 18, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 10, 17, 17, 17, 17, 14, 14, 18, 18, 18, 18, 4, 4] 50 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 587) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N(CCc1ccccn1)Cc1ccncc1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001459613119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459613119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001459613119 none O=C(N(CCc1ccccn1)Cc1ccncc1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 1, 1, 17, 14, 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, 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] 0 hydrogens need 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, 6, 10, 10, 19, 19, 19, 19, 19, 6, 15, 19, 19, 18, 19, 19, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 10, 19, 19, 19, 19, 15, 15, 19, 19, 19, 19, 4, 4] 50 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: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459613119 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459613119 Building ZINC001459636219 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459636219 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/588 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(I)c(Cl)cc1CNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC001459636219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459636219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001459636219 none COc1cc(I)c(Cl)cc1CNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'Cl', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 18, 1, 16, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 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: [50, 44, 44, 44, 44, 44, 44, 44, 44, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 44, 44, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/589 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(I)c(Cl)cc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC001459636219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459636219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001459636219 none COc1cc(I)c(Cl)cc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'Cl', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 18, 1, 16, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 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: [50, 45, 45, 45, 45, 45, 45, 45, 45, 15, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 45, 45, 15, 15, 3, 2, 2, 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]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459636219 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219 Building ZINC001459636219 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459636219 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 588) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1cc(I)c(Cl)cc1CNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC001459636219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459636219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001459636219 none COc1cc(I)c(Cl)cc1CNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'Cl', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 18, 1, 16, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 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: [50, 44, 44, 44, 44, 44, 44, 44, 44, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 44, 44, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3] 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]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 589) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1cc(I)c(Cl)cc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC001459636219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459636219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001459636219 none COc1cc(I)c(Cl)cc1CNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'Cl', '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.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 18, 1, 16, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7, 7, 7, 4, 9, 6, 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: [50, 45, 45, 45, 45, 45, 45, 45, 45, 15, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 50, 50, 50, 45, 45, 15, 15, 3, 2, 2, 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]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459636219 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459636219 Building ZINC001459710372 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459710372 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/590 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1) `ZINC001459710372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459710372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001459710372 none CCC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 45, 45, 45, 45, 45, 7, 5, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 13, 14, 6, 45, 45, 49, 49, 49, 49, 49, 45, 45, 45, 45, 45, 45, 6, 6, 3, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 6, 45, 45, 45, 45] 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, 56, 57, 58, 59, 60]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/591 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1) `ZINC001459710372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459710372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001459710372 none CCC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 47, 7, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 14, 16, 6, 47, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 6, 6, 3, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 6, 47, 47, 47, 47] 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, 56, 57, 58, 59, 60]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/592 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/592' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1) `ZINC001459710372.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459710372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001459710372 none CCC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 47, 47, 47, 47, 7, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 14, 15, 6, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 6, 6, 3, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 6, 47, 47, 47, 47] 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, 56, 57, 58, 59, 60]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/593 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/593' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1) `ZINC001459710372.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459710372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001459710372 none CCC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 47, 7, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 13, 14, 6, 47, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 6, 6, 3, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 6, 47, 47, 47, 47] 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, 56, 57, 58, 59, 60]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459710372 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 Building ZINC001459710372 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459710372 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 590) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1) `ZINC001459710372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459710372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001459710372 none CCC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 45, 45, 45, 45, 45, 7, 5, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 13, 14, 6, 45, 45, 49, 49, 49, 49, 49, 45, 45, 45, 45, 45, 45, 6, 6, 3, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 6, 45, 45, 45, 45] 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, 56, 57, 58, 59, 60]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 591) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1) `ZINC001459710372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459710372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001459710372 none CCC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 47, 7, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 14, 16, 6, 47, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 6, 6, 3, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 6, 47, 47, 47, 47] 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, 56, 57, 58, 59, 60]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 592) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1) `ZINC001459710372.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459710372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001459710372 none CCC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 47, 47, 47, 47, 7, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 14, 15, 6, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 6, 6, 3, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 6, 47, 47, 47, 47] 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, 56, 57, 58, 59, 60]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 593) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1) `ZINC001459710372.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459710372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001459710372 none CCC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 47, 7, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 13, 14, 6, 47, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 6, 6, 3, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 6, 47, 47, 47, 47] 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, 56, 57, 58, 59, 60]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459710372 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 Building ZINC001459710372 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459710372 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 590) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1) `ZINC001459710372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459710372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001459710372 none CCC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 45, 45, 45, 45, 45, 7, 5, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 13, 14, 6, 45, 45, 49, 49, 49, 49, 49, 45, 45, 45, 45, 45, 45, 6, 6, 3, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 6, 45, 45, 45, 45] 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, 56, 57, 58, 59, 60]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 591) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1) `ZINC001459710372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459710372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001459710372 none CCC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 47, 7, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 14, 16, 6, 47, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 6, 6, 3, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 6, 47, 47, 47, 47] 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, 56, 57, 58, 59, 60]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 592) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1) `ZINC001459710372.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459710372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001459710372 none CCC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 47, 47, 47, 47, 7, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 14, 15, 6, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 6, 6, 3, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 6, 47, 47, 47, 47] 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, 56, 57, 58, 59, 60]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 593) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1) `ZINC001459710372.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459710372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001459710372 none CCC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 47, 7, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 13, 14, 6, 47, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 6, 6, 3, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 6, 47, 47, 47, 47] 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, 56, 57, 58, 59, 60]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459710372 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 Building ZINC001459710372 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459710372 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 590) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1) `ZINC001459710372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459710372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001459710372 none CCC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 45, 45, 45, 45, 45, 7, 5, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 13, 14, 6, 45, 45, 49, 49, 49, 49, 49, 45, 45, 45, 45, 45, 45, 6, 6, 3, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 6, 45, 45, 45, 45] 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, 56, 57, 58, 59, 60]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 591) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1) `ZINC001459710372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459710372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001459710372 none CCC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 47, 7, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 14, 16, 6, 47, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 6, 6, 3, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 6, 47, 47, 47, 47] 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, 56, 57, 58, 59, 60]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 592) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1) `ZINC001459710372.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459710372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001459710372 none CCC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 47, 47, 47, 47, 7, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 14, 15, 6, 47, 47, 49, 49, 49, 49, 49, 47, 47, 47, 47, 47, 47, 6, 6, 3, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 6, 47, 47, 47, 47] 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, 56, 57, 58, 59, 60]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 593) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1) `ZINC001459710372.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459710372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001459710372 none CCC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)c(OCC)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 1, 12, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 47, 47, 47, 47, 7, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 6, 6, 13, 14, 6, 47, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 6, 6, 3, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 6, 47, 47, 47, 47] 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, 56, 57, 58, 59, 60]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459710372 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459710372 Building ZINC001459728874 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459728874 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/594 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459728874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728874 none O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 15, 15, 15, 15, 15, 33, 33, 15, 24, 33, 33, 33, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 33, 33, 33, 15, 15, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/595 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459728874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728874 none O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 16, 16, 16, 16, 16, 34, 34, 16, 25, 34, 34, 34, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 34, 34, 34, 16, 16, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/596 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/596' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728874.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459728874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728874 none O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 15, 15, 15, 15, 15, 33, 33, 15, 24, 33, 33, 33, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 33, 33, 33, 15, 15, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/597 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/597' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728874.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459728874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728874 none O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 16, 16, 16, 16, 16, 34, 34, 16, 25, 34, 34, 34, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 34, 34, 34, 16, 16, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459728874 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 Building ZINC001459728874 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459728874 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 594) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459728874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728874 none O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 15, 15, 15, 15, 15, 33, 33, 15, 24, 33, 33, 33, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 33, 33, 33, 15, 15, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 595) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459728874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728874 none O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 16, 16, 16, 16, 16, 34, 34, 16, 25, 34, 34, 34, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 34, 34, 34, 16, 16, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 596) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728874.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459728874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728874 none O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 15, 15, 15, 15, 15, 33, 33, 15, 24, 33, 33, 33, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 33, 33, 33, 15, 15, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 597) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728874.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459728874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728874 none O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 16, 16, 16, 16, 16, 34, 34, 16, 25, 34, 34, 34, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 34, 34, 34, 16, 16, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459728874 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 Building ZINC001459728874 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459728874 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 594) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459728874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728874 none O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 15, 15, 15, 15, 15, 33, 33, 15, 24, 33, 33, 33, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 33, 33, 33, 15, 15, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 595) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459728874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728874 none O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 16, 16, 16, 16, 16, 34, 34, 16, 25, 34, 34, 34, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 34, 34, 34, 16, 16, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 596) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728874.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459728874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728874 none O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 15, 15, 15, 15, 15, 33, 33, 15, 24, 33, 33, 33, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 33, 33, 33, 15, 15, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 597) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728874.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459728874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728874 none O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 16, 16, 16, 16, 16, 34, 34, 16, 25, 34, 34, 34, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 34, 34, 34, 16, 16, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459728874 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 Building ZINC001459728874 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459728874 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 594) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459728874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728874 none O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 15, 15, 15, 15, 15, 33, 33, 15, 24, 33, 33, 33, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 33, 33, 33, 15, 15, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 595) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459728874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728874 none O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 16, 16, 16, 16, 16, 34, 34, 16, 25, 34, 34, 34, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 34, 34, 34, 16, 16, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 596) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728874.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459728874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728874 none O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 15, 15, 15, 15, 15, 33, 33, 15, 24, 33, 33, 33, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 33, 33, 33, 15, 15, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 597) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728874.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459728874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728874 none O=C(N[C@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 16, 16, 16, 16, 16, 34, 34, 16, 25, 34, 34, 34, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 34, 34, 34, 16, 16, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459728874 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728874 Building ZINC001459728876 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459728876 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/598 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459728876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728876 none O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 16, 16, 16, 16, 16, 35, 35, 25, 25, 35, 35, 35, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 35, 35, 35, 16, 16, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/599 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459728876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728876 none O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 15, 15, 15, 15, 15, 31, 31, 22, 22, 31, 31, 31, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 31, 31, 31, 15, 15, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/600 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/600' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728876.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459728876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728876 none O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 16, 16, 16, 16, 16, 35, 35, 25, 25, 35, 35, 35, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 35, 35, 35, 16, 16, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/601 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/601' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728876.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459728876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728876 none O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 15, 15, 15, 15, 15, 31, 31, 22, 22, 31, 31, 31, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 31, 31, 31, 15, 15, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459728876 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 Building ZINC001459728876 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459728876 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 598) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459728876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728876 none O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 16, 16, 16, 16, 16, 35, 35, 25, 25, 35, 35, 35, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 35, 35, 35, 16, 16, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 599) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459728876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728876 none O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 15, 15, 15, 15, 15, 31, 31, 22, 22, 31, 31, 31, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 31, 31, 31, 15, 15, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 600) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728876.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459728876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728876 none O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 16, 16, 16, 16, 16, 35, 35, 25, 25, 35, 35, 35, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 35, 35, 35, 16, 16, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 601) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728876.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459728876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728876 none O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 15, 15, 15, 15, 15, 31, 31, 22, 22, 31, 31, 31, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 31, 31, 31, 15, 15, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459728876 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 Building ZINC001459728876 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459728876 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 598) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459728876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728876 none O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 16, 16, 16, 16, 16, 35, 35, 25, 25, 35, 35, 35, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 35, 35, 35, 16, 16, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 599) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459728876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728876 none O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 15, 15, 15, 15, 15, 31, 31, 22, 22, 31, 31, 31, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 31, 31, 31, 15, 15, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 600) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728876.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459728876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728876 none O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 16, 16, 16, 16, 16, 35, 35, 25, 25, 35, 35, 35, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 35, 35, 35, 16, 16, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 601) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728876.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459728876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728876 none O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 15, 15, 15, 15, 15, 31, 31, 22, 22, 31, 31, 31, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 31, 31, 31, 15, 15, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459728876 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 Building ZINC001459728876 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001459728876 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 598) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459728876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728876 none O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 16, 16, 16, 16, 16, 35, 35, 25, 25, 35, 35, 35, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 35, 35, 35, 16, 16, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 599) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459728876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728876 none O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 15, 15, 15, 15, 15, 31, 31, 22, 22, 31, 31, 31, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 31, 31, 31, 15, 15, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 600) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728876.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001459728876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728876 none O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 16, 16, 16, 16, 16, 35, 35, 25, 25, 35, 35, 35, 16, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 16, 16, 16, 16, 35, 35, 35, 16, 16, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 601) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001459728876.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001459728876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001459728876 none O=C(N[C@@H]1CCN(c2ccc(Cl)cc2Cl)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 4, 15, 15, 15, 15, 15, 31, 31, 22, 22, 31, 31, 31, 15, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 15, 15, 15, 15, 31, 31, 31, 15, 15, 6, 6, 6, 6, 6, 6, 6] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459728876 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459728876 Building ZINC001459759413 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459759413 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/602 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC=C(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001459759413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459759413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001459759413 none CC(C)(C)OC(=O)N1CC=C(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 45, 47, 45, 45, 34, 16, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 45, 45, 47, 47, 47, 47, 47, 47, 47, 47, 47, 45, 45, 45, 16, 16, 10, 10, 2, 5, 5, 45, 45, 45, 45] 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/603 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC=C(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001459759413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459759413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001459759413 none CC(C)(C)OC(=O)N1CC=C(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 45, 47, 45, 45, 34, 16, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 45, 45, 47, 47, 47, 47, 47, 47, 47, 47, 47, 45, 45, 45, 16, 16, 10, 10, 2, 5, 5, 45, 45, 45, 45] 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459759413 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413 Building ZINC001459759413 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459759413 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 602) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC=C(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001459759413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459759413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001459759413 none CC(C)(C)OC(=O)N1CC=C(CCNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 45, 47, 45, 45, 34, 16, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 45, 45, 47, 47, 47, 47, 47, 47, 47, 47, 47, 45, 45, 45, 16, 16, 10, 10, 2, 5, 5, 45, 45, 45, 45] 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 603) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC=C(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001459759413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459759413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001459759413 none CC(C)(C)OC(=O)N1CC=C(CCNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', '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', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 45, 47, 45, 45, 34, 16, 10, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 45, 45, 47, 47, 47, 47, 47, 47, 47, 47, 47, 45, 45, 45, 16, 16, 10, 10, 2, 5, 5, 45, 45, 45, 45] 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459759413 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459759413 Building ZINC001459848151 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459848151 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/604 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1Br) `ZINC001459848151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459848151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001459848151 none COC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 17, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 12, 32, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 12, 12, 32, 32, 32, 12, 12, 12, 4, 9, 9] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/605 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1Br) `ZINC001459848151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459848151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001459848151 none COC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 17, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 12, 33, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 12, 12, 33, 33, 33, 12, 12, 12, 4, 9, 9] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459848151 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151 Building ZINC001459848151 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459848151 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 604) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1Br) `ZINC001459848151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459848151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001459848151 none COC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 17, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 12, 32, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 12, 12, 32, 32, 32, 12, 12, 12, 4, 9, 9] 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 605) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1Br) `ZINC001459848151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459848151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001459848151 none COC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 17, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 12, 33, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 12, 12, 33, 33, 33, 12, 12, 12, 4, 9, 9] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459848151 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459848151 Building ZINC001459887480 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459887480 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/606 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3c(C)cc(Br)cc3C)C2=O)cc1) `ZINC001459887480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459887480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459887480 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3c(C)cc(Br)cc3C)C2=O)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', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 5, 1, 1, 17, 1, 1, 5, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 10, 47, 47, 47, 47, 47, 47, 50, 50, 50, 47, 48, 50, 50, 50, 47, 47, 5, 5, 5, 5, 5, 5, 5, 5, 47, 47, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 5, 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]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/607 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3c(C)cc(Br)cc3C)C2=O)cc1) `ZINC001459887480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459887480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459887480 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3c(C)cc(Br)cc3C)C2=O)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', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 5, 1, 1, 17, 1, 1, 5, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 5, 5, 11, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459887480 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480 Building ZINC001459887480 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459887480 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 606) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3c(C)cc(Br)cc3C)C2=O)cc1) `ZINC001459887480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459887480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459887480 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3c(C)cc(Br)cc3C)C2=O)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', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 5, 1, 1, 17, 1, 1, 5, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 10, 47, 47, 47, 47, 47, 47, 50, 50, 50, 47, 48, 50, 50, 50, 47, 47, 5, 5, 5, 5, 5, 5, 5, 5, 47, 47, 47, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 5, 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]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 607) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3c(C)cc(Br)cc3C)C2=O)cc1) `ZINC001459887480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459887480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459887480 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(c3c(C)cc(Br)cc3C)C2=O)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', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 5, 1, 1, 17, 1, 1, 5, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 5, 5, 11, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459887480 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887480 Building ZINC001459887498 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459887498 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/608 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3c(C)cc(Br)cc3C)C2=O)cc1) `ZINC001459887498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459887498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459887498 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3c(C)cc(Br)cc3C)C2=O)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', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 5, 1, 1, 17, 1, 1, 5, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 1, 1, 1, 1, 5, 5, 6, 47, 47, 47, 47, 47, 47, 48, 48, 48, 47, 47, 48, 48, 48, 47, 47, 4, 4, 4, 4, 4, 4, 4, 5, 47, 47, 47, 47, 47, 47, 48, 48, 48, 48, 48, 48, 48, 48, 4, 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]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/609 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3c(C)cc(Br)cc3C)C2=O)cc1) `ZINC001459887498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459887498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459887498 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3c(C)cc(Br)cc3C)C2=O)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', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 5, 1, 1, 17, 1, 1, 5, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 5, 46, 46, 46, 46, 46, 46, 48, 48, 48, 47, 46, 48, 48, 48, 46, 46, 5, 5, 5, 5, 5, 5, 5, 5, 46, 46, 46, 46, 46, 46, 48, 48, 48, 48, 48, 48, 48, 48, 5, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459887498 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498 Building ZINC001459887498 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459887498 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 608) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3c(C)cc(Br)cc3C)C2=O)cc1) `ZINC001459887498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459887498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459887498 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3c(C)cc(Br)cc3C)C2=O)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', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 5, 1, 1, 17, 1, 1, 5, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 1, 1, 1, 1, 5, 5, 6, 47, 47, 47, 47, 47, 47, 48, 48, 48, 47, 47, 48, 48, 48, 47, 47, 4, 4, 4, 4, 4, 4, 4, 5, 47, 47, 47, 47, 47, 47, 48, 48, 48, 48, 48, 48, 48, 48, 4, 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]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 609) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3c(C)cc(Br)cc3C)C2=O)cc1) `ZINC001459887498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459887498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001459887498 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(c3c(C)cc(Br)cc3C)C2=O)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', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 5, 1, 1, 17, 1, 1, 5, 1, 11, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 5, 5, 5, 46, 46, 46, 46, 46, 46, 48, 48, 48, 47, 46, 48, 48, 48, 46, 46, 5, 5, 5, 5, 5, 5, 5, 5, 46, 46, 46, 46, 46, 46, 48, 48, 48, 48, 48, 48, 48, 48, 5, 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459887498 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459887498 Building ZINC001459971181 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459971181 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/610 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/610' -> `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)NCC(C)(C)Oc1cc(F)cc(F)c1) `ZINC001459971181.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459971181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001459971181 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)Oc1cc(F)cc(F)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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', '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, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 9, 18, 19, 20, 48, 48, 48, 48, 48, 48, 48, 48, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 9, 9, 20, 20, 20, 20, 20, 20, 48, 48, 48] 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, 50, 51, 52, 53]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/611 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/611' -> `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)NCC(C)(C)Oc1cc(F)cc(F)c1) `ZINC001459971181.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459971181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001459971181 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)Oc1cc(F)cc(F)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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', '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, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 3, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 19, 18, 19, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 19, 19, 19, 19, 19, 19, 50, 50, 50] 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, 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/6899/xaj-8058088.10/working/building/ZINC001459971181 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459971181 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181 Building ZINC001459971181 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001459971181 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 610) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)Oc1cc(F)cc(F)c1) `ZINC001459971181.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001459971181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001459971181 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC(C)(C)Oc1cc(F)cc(F)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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', '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, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 9, 18, 19, 20, 48, 48, 48, 48, 48, 48, 48, 48, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 9, 9, 20, 20, 20, 20, 20, 20, 48, 48, 48] 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, 50, 51, 52, 53]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 611) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)Oc1cc(F)cc(F)c1) `ZINC001459971181.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001459971181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001459971181 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC(C)(C)Oc1cc(F)cc(F)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.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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', '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, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 3, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 19, 18, 19, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 19, 19, 19, 19, 19, 19, 50, 50, 50] 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, 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/6899/xaj-8058088.10/working/building/ZINC001459971181 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001459971181 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001459971181 Building ZINC001460106945 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460106945 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/612 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(N2CCOCC2)ccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001460106945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460106945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001460106945 none O=C(Nc1cc(N2CCOCC2)ccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 14, 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, 3, 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] 0 hydrogens need 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, 9, 9, 13, 34, 34, 34, 34, 34, 9, 9, 9, 9, 1, 1, 1, 6, 6, 6, 6, 6, 4, 9, 34, 34, 34, 34, 34, 34, 34, 34, 9, 9, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/613 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(N2CCOCC2)ccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001460106945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460106945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001460106945 none O=C(Nc1cc(N2CCOCC2)ccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 14, 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, 3, 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] 0 hydrogens need 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, 10, 10, 14, 33, 33, 33, 33, 33, 10, 10, 10, 10, 1, 1, 1, 7, 7, 7, 7, 7, 4, 10, 33, 33, 33, 33, 33, 33, 33, 33, 10, 10, 7, 7] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460106945 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945 Building ZINC001460106945 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460106945 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 612) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1cc(N2CCOCC2)ccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001460106945.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460106945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001460106945 none O=C(Nc1cc(N2CCOCC2)ccc1Br)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 14, 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, 3, 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] 0 hydrogens need 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, 9, 9, 13, 34, 34, 34, 34, 34, 9, 9, 9, 9, 1, 1, 1, 6, 6, 6, 6, 6, 4, 9, 34, 34, 34, 34, 34, 34, 34, 34, 9, 9, 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 613) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1cc(N2CCOCC2)ccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001460106945.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460106945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001460106945 none O=C(Nc1cc(N2CCOCC2)ccc1Br)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 17, 5, 12, 1, 1, 1, 1, 16, 14, 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, 3, 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] 0 hydrogens need 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, 10, 10, 14, 33, 33, 33, 33, 33, 10, 10, 10, 10, 1, 1, 1, 7, 7, 7, 7, 7, 4, 10, 33, 33, 33, 33, 33, 33, 33, 33, 10, 10, 7, 7] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460106945 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460106945 Building ZINC001460107127 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460107127 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/614 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2nc(C(F)(F)F)c(I)s2)c1) `ZINC001460107127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460107127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001460107127 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2nc(C(F)(F)F)c(I)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'I', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 15, 15, 15, 1, 18, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 1, 11, 11, 8, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/615 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2nc(C(F)(F)F)c(I)s2)c1) `ZINC001460107127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460107127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001460107127 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2nc(C(F)(F)F)c(I)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'I', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 15, 15, 15, 1, 18, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 11, 11, 11, 8, 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460107127 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127 Building ZINC001460107127 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460107127 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 614) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2nc(C(F)(F)F)c(I)s2)c1) `ZINC001460107127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460107127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001460107127 none Cc1cccc([C@@]([O-])([SiH3])C(=O)Nc2nc(C(F)(F)F)c(I)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'I', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 15, 15, 15, 1, 18, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 1, 11, 11, 8, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 615) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2nc(C(F)(F)F)c(I)s2)c1) `ZINC001460107127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460107127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001460107127 none Cc1cccc([C@]([O-])([SiH3])C(=O)Nc2nc(C(F)(F)F)c(I)s2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'I', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 15, 15, 15, 1, 18, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 11, 11, 11, 8, 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460107127 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460107127 Building ZINC001460242622 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460242622 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/616 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](Cc3cccc(I)c3)C2)cc1) `ZINC001460242622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460242622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001460242622 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](Cc3cccc(I)c3)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.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 18, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 2, 2, 1, 1, 1, 1, 2, 4, 13, 13, 13, 13, 13, 27, 50, 50, 48, 50, 50, 50, 13, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 27, 27, 50, 50, 50, 50, 13, 13, 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]) total number of confs: 154 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/617 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](Cc3cccc(I)c3)C2)cc1) `ZINC001460242622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460242622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001460242622 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](Cc3cccc(I)c3)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.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 18, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 2, 2, 1, 1, 1, 1, 2, 3, 12, 12, 12, 12, 12, 28, 50, 50, 49, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 28, 28, 50, 50, 50, 50, 12, 12, 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]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460242622 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622 Building ZINC001460242622 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460242622 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 616) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](Cc3cccc(I)c3)C2)cc1) `ZINC001460242622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460242622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001460242622 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](Cc3cccc(I)c3)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.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 18, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 2, 2, 1, 1, 1, 1, 2, 4, 13, 13, 13, 13, 13, 27, 50, 50, 48, 50, 50, 50, 13, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 27, 27, 50, 50, 50, 50, 13, 13, 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]) total number of confs: 154 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 617) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](Cc3cccc(I)c3)C2)cc1) `ZINC001460242622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460242622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001460242622 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](Cc3cccc(I)c3)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.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 18, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 2, 2, 1, 1, 1, 1, 2, 3, 12, 12, 12, 12, 12, 28, 50, 50, 49, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 28, 28, 50, 50, 50, 50, 12, 12, 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]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460242622 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242622 Building ZINC001460242623 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460242623 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/618 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](Cc3cccc(I)c3)C2)cc1) `ZINC001460242623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460242623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001460242623 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](Cc3cccc(I)c3)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.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 18, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 2, 2, 1, 1, 1, 1, 2, 3, 12, 12, 12, 12, 12, 28, 50, 50, 49, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 28, 28, 50, 50, 50, 50, 12, 12, 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]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/619 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](Cc3cccc(I)c3)C2)cc1) `ZINC001460242623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460242623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001460242623 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](Cc3cccc(I)c3)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.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 18, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 2, 2, 1, 1, 1, 1, 2, 4, 13, 13, 13, 13, 13, 26, 50, 50, 48, 50, 50, 50, 13, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 26, 26, 50, 50, 50, 50, 13, 13, 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]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460242623 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623 Building ZINC001460242623 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460242623 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 618) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](Cc3cccc(I)c3)C2)cc1) `ZINC001460242623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460242623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001460242623 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](Cc3cccc(I)c3)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.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 18, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 2, 2, 1, 1, 1, 1, 2, 3, 12, 12, 12, 12, 12, 28, 50, 50, 49, 50, 50, 50, 12, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 28, 28, 50, 50, 50, 50, 12, 12, 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]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 619) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](Cc3cccc(I)c3)C2)cc1) `ZINC001460242623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460242623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001460242623 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CC[C@H](Cc3cccc(I)c3)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.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 18, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [1, 1, 2, 2, 1, 1, 1, 1, 2, 4, 13, 13, 13, 13, 13, 26, 50, 50, 48, 50, 50, 50, 13, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 26, 26, 50, 50, 50, 50, 13, 13, 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]) total number of confs: 150 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460242623 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460242623 Building ZINC001460284518 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460284518 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/620 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C(F)(F)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccccc1) `ZINC001460284518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460284518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001460284518 none CCOC(=O)C(F)(F)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'F', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 15, 15, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 15, 3, 6, 6, 3, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 7, 3, 3, 3, 3, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 3, 3, 3, 7, 7, 7, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/621 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C(F)(F)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccccc1) `ZINC001460284518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460284518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001460284518 none CCOC(=O)C(F)(F)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'F', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 15, 15, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 12, 5, 12, 3, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 4, 4, 4, 3, 4, 4, 3, 4, 4, 20, 20, 20, 20, 20, 3, 4, 4, 10, 10, 10, 4, 4, 4, 3, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 99 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460284518 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518 Building ZINC001460284518 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460284518 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 620) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)C(F)(F)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccccc1) `ZINC001460284518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460284518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001460284518 none CCOC(=O)C(F)(F)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'F', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 15, 15, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 15, 3, 6, 6, 3, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 7, 3, 3, 3, 3, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 3, 3, 3, 7, 7, 7, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 120 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 621) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)C(F)(F)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccccc1) `ZINC001460284518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460284518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001460284518 none CCOC(=O)C(F)(F)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'F', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 15, 15, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 12, 5, 12, 3, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 4, 4, 4, 3, 4, 4, 3, 4, 4, 20, 20, 20, 20, 20, 3, 4, 4, 10, 10, 10, 4, 4, 4, 3, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 99 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460284518 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284518 Building ZINC001460284522 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460284522 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/622 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C(F)(F)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccccc1) `ZINC001460284522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460284522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001460284522 none CCOC(=O)C(F)(F)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'F', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 15, 15, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 5, 11, 3, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 11, 4, 4, 4, 3, 4, 4, 3, 4, 4, 19, 19, 19, 19, 19, 3, 4, 4, 11, 11, 11, 4, 4, 4, 3, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 108 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/623 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C(F)(F)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccccc1) `ZINC001460284522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460284522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001460284522 none CCOC(=O)C(F)(F)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'F', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 15, 15, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 15, 3, 6, 6, 3, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 7, 3, 3, 3, 3, 6, 6, 3, 6, 6, 24, 24, 24, 24, 24, 3, 3, 3, 7, 7, 7, 3, 6, 6, 3, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460284522 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522 Building ZINC001460284522 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460284522 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 622) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C(F)(F)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccccc1) `ZINC001460284522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460284522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001460284522 none CCOC(=O)C(F)(F)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'F', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 15, 15, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 5, 11, 3, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 11, 4, 4, 4, 3, 4, 4, 3, 4, 4, 19, 19, 19, 19, 19, 3, 4, 4, 11, 11, 11, 4, 4, 4, 3, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 108 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 623) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C(F)(F)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccccc1) `ZINC001460284522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460284522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001460284522 none CCOC(=O)C(F)(F)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'F', 'F', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 15, 15, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 15, 3, 6, 6, 3, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 7, 3, 3, 3, 3, 6, 6, 3, 6, 6, 24, 24, 24, 24, 24, 3, 3, 3, 7, 7, 7, 3, 6, 6, 3, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460284522 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460284522 Building ZINC001460632745 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460632745 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/624 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(Br)c(F)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001460632745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460632745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001460632745 none CCOc1cc(Br)c(F)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 31, 31, 31, 31, 31, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/625 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1cc(Br)c(F)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001460632745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460632745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001460632745 none CCOc1cc(Br)c(F)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 19, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460632745 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745 Building ZINC001460632745 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460632745 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 624) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOc1cc(Br)c(F)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001460632745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460632745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001460632745 none CCOc1cc(Br)c(F)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 31, 31, 31, 31, 31, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 625) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOc1cc(Br)c(F)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001460632745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460632745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001460632745 none CCOc1cc(Br)c(F)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 17, 1, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7] 0 hydrogens 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, 19, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460632745 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460632745 Building ZINC001460682800 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460682800 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/626 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccn(Cc2c(F)cccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1=O) `ZINC001460682800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460682800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001460682800 none Cc1cccn(Cc2c(F)cccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 29, 13, 13, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 29, 29, 13, 13, 13, 4, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/627 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccn(Cc2c(F)cccc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1=O) `ZINC001460682800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460682800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001460682800 none Cc1cccn(Cc2c(F)cccc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 29, 13, 13, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 36, 36, 36, 36, 36, 36, 36, 36, 29, 29, 13, 13, 13, 4, 8, 8] 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]) total number of confs: 111 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460682800 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800 Building ZINC001460682800 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460682800 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 626) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccn(Cc2c(F)cccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1=O) `ZINC001460682800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460682800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001460682800 none Cc1cccn(Cc2c(F)cccc2NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 29, 13, 13, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 29, 29, 13, 13, 13, 4, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 627) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccn(Cc2c(F)cccc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1=O) `ZINC001460682800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460682800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001460682800 none Cc1cccn(Cc2c(F)cccc2NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 29, 13, 13, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 36, 36, 36, 36, 36, 36, 36, 36, 29, 29, 13, 13, 13, 4, 8, 8] 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]) total number of confs: 111 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460682800 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460682800 Building ZINC001460733843 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460733843 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/628 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)[C@H](c2ccccc2)C1) `ZINC001460733843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460733843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001460733843 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)[C@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 16, 8, 8, 8, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 8, 8, 8, 9, 9, 9, 9, 9, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 9, 9, 9, 9, 9, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/629 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)[C@H](c2ccccc2)C1) `ZINC001460733843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460733843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001460733843 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)[C@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 7, 19, 7, 7, 7, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 7, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460733843 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843 Building ZINC001460733843 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460733843 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 628) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)[C@H](c2ccccc2)C1) `ZINC001460733843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460733843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001460733843 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)[C@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 8, 16, 8, 8, 8, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 8, 8, 8, 9, 9, 9, 9, 9, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 9, 9, 9, 9, 9, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 629) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)[C@H](c2ccccc2)C1) `ZINC001460733843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460733843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001460733843 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)[C@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 7, 19, 7, 7, 7, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 7, 7, 7, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 84 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460733843 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733843 Building ZINC001460733845 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460733845 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/630 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)[C@@H](c2ccccc2)C1) `ZINC001460733845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460733845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001460733845 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 7, 18, 7, 7, 7, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/631 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)[C@@H](c2ccccc2)C1) `ZINC001460733845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460733845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001460733845 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 8, 18, 8, 8, 8, 7, 1, 7, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 3, 8, 8, 8, 9, 9, 8, 9, 9, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 9, 9, 8, 9, 9, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460733845 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845 Building ZINC001460733845 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460733845 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 630) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)[C@@H](c2ccccc2)C1) `ZINC001460733845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460733845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001460733845 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 7, 18, 7, 7, 7, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 631) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)[C@@H](c2ccccc2)C1) `ZINC001460733845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460733845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001460733845 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 8, 18, 8, 8, 8, 7, 1, 7, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 3, 8, 8, 8, 9, 9, 8, 9, 9, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 9, 9, 8, 9, 9, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460733845 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460733845 Building ZINC001460741001 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460741001 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/632 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/632' -> `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)NCCc1cccc(Br)c1) `ZINC001460741001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460741001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001460741001 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1cccc(Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 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, 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, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 24, 41, 41, 41, 41, 41, 41, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 16, 16, 24, 24, 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: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/633 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/633' -> `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)NCCc1cccc(Br)c1) `ZINC001460741001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460741001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001460741001 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1cccc(Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 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, 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, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 23, 40, 40, 40, 40, 40, 40, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 15, 15, 23, 23, 40, 40, 40, 40] 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: 138 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460741001 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001 Building ZINC001460741001 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460741001 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 632) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1cccc(Br)c1) `ZINC001460741001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460741001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001460741001 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1cccc(Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 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, 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, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 24, 41, 41, 41, 41, 41, 41, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 3, 16, 16, 24, 24, 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: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 633) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1cccc(Br)c1) `ZINC001460741001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460741001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001460741001 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1cccc(Br)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 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, 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, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 23, 40, 40, 40, 40, 40, 40, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 15, 15, 23, 23, 40, 40, 40, 40] 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: 138 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460741001 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460741001 Building ZINC001460802898 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460802898 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/634 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(c1ccnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1)C1CCCC1) `ZINC001460802898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460802898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001460802898 none CCN(c1ccnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 5, 31, 41, 41, 41, 41, 39, 39, 39, 39, 39, 5, 5, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 41, 41, 41, 41, 41, 41, 41, 41, 41] 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, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/635 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(c1ccnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1)C1CCCC1) `ZINC001460802898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460802898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001460802898 none CCN(c1ccnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 5, 31, 40, 40, 40, 40, 38, 38, 38, 38, 38, 5, 5, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 40, 40, 40, 40, 40, 40, 40, 40, 40] 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, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 152 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460802898 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898 Building ZINC001460802898 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460802898 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 634) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(c1ccnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1)C1CCCC1) `ZINC001460802898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460802898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001460802898 none CCN(c1ccnc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 5, 31, 41, 41, 41, 41, 39, 39, 39, 39, 39, 5, 5, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 41, 41, 41, 41, 41, 41, 41, 41, 41] 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, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 635) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(c1ccnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1)C1CCCC1) `ZINC001460802898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460802898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001460802898 none CCN(c1ccnc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'N.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'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 5, 31, 40, 40, 40, 40, 38, 38, 38, 38, 38, 5, 5, 2, 2, 2, 2, 3, 3, 2, 3, 3, 2, 2, 2, 40, 40, 40, 40, 40, 40, 40, 40, 40] 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, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 152 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460802898 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460802898 Building ZINC001460851404 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460851404 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/636 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NS(=O)(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001460851404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460851404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001460851404 none CC(C)(C)NS(=O)(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 5, 25, 25, 5, 25, 25, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 5, 4, 2, 4, 25, 25] 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/637 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)NS(=O)(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001460851404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460851404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001460851404 none CC(C)(C)NS(=O)(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 23, 5, 23, 23, 5, 23, 23, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 23, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 23, 23, 5, 5, 1, 5, 23, 23] 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, 42, 43, 44]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460851404 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404 Building ZINC001460851404 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460851404 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 636) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)NS(=O)(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001460851404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460851404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001460851404 none CC(C)(C)NS(=O)(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 5, 25, 25, 5, 25, 25, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 25, 25, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 25, 25, 5, 4, 2, 4, 25, 25] 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]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 637) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)NS(=O)(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1) `ZINC001460851404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460851404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001460851404 none CC(C)(C)NS(=O)(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.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, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 23, 5, 23, 23, 5, 23, 23, 5, 5, 1, 5, 1, 1, 1, 5, 5, 5, 1, 5, 5, 5, 23, 23, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 23, 23, 5, 5, 1, 5, 23, 23] 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, 42, 43, 44]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460851404 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460851404 Building ZINC001460892919 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460892919 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/638 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Br)c(F)cc1N1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001460892919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460892919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001460892919 none O=C(Nc1cc(Br)c(F)cc1N1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 17, 1, 15, 1, 1, 8, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 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, 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] 0 hydrogens 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, 6, 6, 20, 20, 20, 9, 20, 20, 20, 30, 50, 50, 50, 50, 49, 1, 1, 1, 4, 4, 4, 4, 4, 4, 6, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 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]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/639 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(Br)c(F)cc1N1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001460892919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460892919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001460892919 none O=C(Nc1cc(Br)c(F)cc1N1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 17, 1, 15, 1, 1, 8, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 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, 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] 0 hydrogens 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, 6, 6, 20, 20, 20, 10, 20, 20, 20, 29, 50, 50, 50, 50, 49, 1, 1, 1, 4, 4, 1, 2, 4, 4, 6, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 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]) total number of confs: 144 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460892919 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919 Building ZINC001460892919 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001460892919 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 638) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1cc(Br)c(F)cc1N1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001460892919.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001460892919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001460892919 none O=C(Nc1cc(Br)c(F)cc1N1CCOCC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 17, 1, 15, 1, 1, 8, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 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, 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] 0 hydrogens 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, 6, 6, 20, 20, 20, 9, 20, 20, 20, 30, 50, 50, 50, 50, 49, 1, 1, 1, 4, 4, 4, 4, 4, 4, 6, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 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]) total number of confs: 136 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 639) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1cc(Br)c(F)cc1N1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001460892919.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001460892919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001460892919 none O=C(Nc1cc(Br)c(F)cc1N1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 1, 1, 1, 17, 1, 15, 1, 1, 8, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 16, 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, 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] 0 hydrogens 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, 6, 6, 20, 20, 20, 10, 20, 20, 20, 29, 50, 50, 50, 50, 49, 1, 1, 1, 4, 4, 1, 2, 4, 4, 6, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4] 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]) total number of confs: 144 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001460892919 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001460892919 Building ZINC001461089310 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461089310 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/640 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(CCCn2ccnc2)c2ccc(Br)cn2)cc1) `ZINC001461089310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461089310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461089310 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N(CCCn2ccnc2)c2ccc(Br)cn2)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 5, 8, 10, 14, 43, 43, 43, 43, 5, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 8, 8, 10, 10, 14, 14, 43, 43, 43, 12, 12, 12, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/641 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N(CCCn2ccnc2)c2ccc(Br)cn2)cc1) `ZINC001461089310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461089310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461089310 none Cc1ccc([C@]([O-])([SiH3])C(=O)N(CCCn2ccnc2)c2ccc(Br)cn2)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 5, 8, 10, 14, 43, 43, 43, 43, 5, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 8, 8, 10, 10, 14, 14, 43, 43, 43, 13, 13, 13, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461089310 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310 Building ZINC001461089310 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461089310 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 640) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(CCCn2ccnc2)c2ccc(Br)cn2)cc1) `ZINC001461089310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461089310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461089310 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N(CCCn2ccnc2)c2ccc(Br)cn2)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 5, 8, 10, 14, 43, 43, 43, 43, 5, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 8, 8, 10, 10, 14, 14, 43, 43, 43, 12, 12, 12, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 641) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N(CCCn2ccnc2)c2ccc(Br)cn2)cc1) `ZINC001461089310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461089310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001461089310 none Cc1ccc([C@]([O-])([SiH3])C(=O)N(CCCn2ccnc2)c2ccc(Br)cn2)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 5, 8, 10, 14, 43, 43, 43, 43, 5, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 8, 8, 10, 10, 14, 14, 43, 43, 43, 13, 13, 13, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461089310 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461089310 Building ZINC001461125587 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461125587 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/642 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cnc(c3ccc(Br)s3)nc2)cn1) `ZINC001461125587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461125587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001461125587 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cnc(c3ccc(Br)s3)nc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 1, 1, 17, 14, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 15, 15, 9, 9, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 3, 20, 20, 20, 22, 20, 6, 6, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 3, 6, 20, 20, 6, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/643 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cnc(c3ccc(Br)s3)nc2)cn1) `ZINC001461125587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461125587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001461125587 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cnc(c3ccc(Br)s3)nc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 1, 1, 17, 14, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 15, 15, 7, 7, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 3, 21, 21, 21, 21, 21, 6, 6, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 3, 6, 21, 21, 6, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461125587 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587 Building ZINC001461125587 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461125587 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 642) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cnc(c3ccc(Br)s3)nc2)cn1) `ZINC001461125587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461125587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001461125587 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2cnc(c3ccc(Br)s3)nc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 1, 1, 17, 14, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 15, 15, 9, 9, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 3, 20, 20, 20, 22, 20, 6, 6, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 3, 6, 20, 20, 6, 9] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 643) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cnc(c3ccc(Br)s3)nc2)cn1) `ZINC001461125587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461125587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001461125587 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2cnc(c3ccc(Br)s3)nc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 1, 1, 17, 14, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 15, 15, 7, 7, 1, 1, 1, 1, 3, 3, 3, 6, 6, 3, 3, 21, 21, 21, 21, 21, 6, 6, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 3, 6, 21, 21, 6, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461125587 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461125587 Building ZINC001461165242 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461165242 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/644 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/644' -> `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](COCc1ccccc1)C(=O)OCc1ccccc1) `ZINC001461165242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461165242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001461165242 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](COCc1ccccc1)C(=O)OCc1ccccc1 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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 3, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 8, 13, 30, 38, 38, 30, 38, 38, 5, 5, 5, 6, 15, 20, 20, 16, 20, 20, 2, 2, 2, 2, 2, 2, 3, 8, 8, 30, 30, 38, 38, 30, 38, 38, 15, 15, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/645 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/645' -> `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](COCc1ccccc1)C(=O)OCc1ccccc1) `ZINC001461165242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461165242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001461165242 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](COCc1ccccc1)C(=O)OCc1ccccc1 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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 3, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 9, 15, 27, 33, 33, 27, 33, 33, 7, 7, 7, 7, 19, 25, 25, 19, 25, 25, 2, 2, 2, 2, 2, 2, 3, 9, 9, 27, 27, 33, 33, 27, 33, 33, 19, 19, 25, 25, 19, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461165242 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242 Building ZINC001461165242 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461165242 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 644) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](COCc1ccccc1)C(=O)OCc1ccccc1) `ZINC001461165242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461165242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001461165242 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@H](COCc1ccccc1)C(=O)OCc1ccccc1 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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 3, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 8, 13, 30, 38, 38, 30, 38, 38, 5, 5, 5, 6, 15, 20, 20, 16, 20, 20, 2, 2, 2, 2, 2, 2, 3, 8, 8, 30, 30, 38, 38, 30, 38, 38, 15, 15, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 645) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](COCc1ccccc1)C(=O)OCc1ccccc1) `ZINC001461165242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461165242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001461165242 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@H](COCc1ccccc1)C(=O)OCc1ccccc1 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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 3, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 7, 7, 9, 15, 27, 33, 33, 27, 33, 33, 7, 7, 7, 7, 19, 25, 25, 19, 25, 25, 2, 2, 2, 2, 2, 2, 3, 9, 9, 27, 27, 33, 33, 27, 33, 33, 19, 19, 25, 25, 19, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461165242 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165242 Building ZINC001461165247 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461165247 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/646 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/646' -> `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](COCc1ccccc1)C(=O)OCc1ccccc1) `ZINC001461165247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461165247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001461165247 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](COCc1ccccc1)C(=O)OCc1ccccc1 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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 3, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 11, 16, 28, 36, 36, 32, 36, 36, 8, 8, 8, 8, 19, 25, 25, 19, 25, 25, 2, 2, 2, 2, 2, 2, 3, 11, 11, 28, 28, 36, 36, 36, 36, 36, 19, 19, 25, 25, 19, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/647 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/647' -> `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](COCc1ccccc1)C(=O)OCc1ccccc1) `ZINC001461165247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461165247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001461165247 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](COCc1ccccc1)C(=O)OCc1ccccc1 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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 3, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 8, 13, 29, 37, 37, 31, 37, 37, 5, 5, 5, 6, 15, 20, 20, 15, 20, 20, 2, 2, 2, 2, 2, 2, 3, 8, 8, 29, 29, 37, 37, 37, 37, 37, 15, 15, 20, 20, 15, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461165247 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247 Building ZINC001461165247 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461165247 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 646) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](COCc1ccccc1)C(=O)OCc1ccccc1) `ZINC001461165247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461165247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001461165247 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H](COCc1ccccc1)C(=O)OCc1ccccc1 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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 3, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 8, 8, 11, 16, 28, 36, 36, 32, 36, 36, 8, 8, 8, 8, 19, 25, 25, 19, 25, 25, 2, 2, 2, 2, 2, 2, 3, 11, 11, 28, 28, 36, 36, 36, 36, 36, 19, 19, 25, 25, 19, 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, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 647) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](COCc1ccccc1)C(=O)OCc1ccccc1) `ZINC001461165247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461165247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001461165247 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H](COCc1ccccc1)C(=O)OCc1ccccc1 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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 3, 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: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 8, 13, 29, 37, 37, 31, 37, 37, 5, 5, 5, 6, 15, 20, 20, 15, 20, 20, 2, 2, 2, 2, 2, 2, 3, 8, 8, 29, 29, 37, 37, 37, 37, 37, 15, 15, 20, 20, 15, 20, 20] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461165247 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461165247 Building ZINC001461299103 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461299103 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/648 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(c2cccc(Br)c2)n1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001461299103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461299103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001461299103 none O=C(Nc1ccnc(c2cccc(Br)c2)n1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', '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, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 28, 28, 10, 28, 28, 28, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 5, 5, 28, 28, 28, 28, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/649 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(c2cccc(Br)c2)n1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001461299103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461299103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001461299103 none O=C(Nc1ccnc(c2cccc(Br)c2)n1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', '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, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 27, 27, 22, 27, 27, 27, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 5, 5, 27, 27, 27, 27, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461299103 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103 Building ZINC001461299103 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461299103 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 648) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccnc(c2cccc(Br)c2)n1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001461299103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461299103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001461299103 none O=C(Nc1ccnc(c2cccc(Br)c2)n1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', '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, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 28, 28, 10, 28, 28, 28, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 5, 5, 28, 28, 28, 28, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 649) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccnc(c2cccc(Br)c2)n1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001461299103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461299103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001461299103 none O=C(Nc1ccnc(c2cccc(Br)c2)n1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.3', '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, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 27, 27, 22, 27, 27, 27, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 5, 5, 27, 27, 27, 27, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461299103 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461299103 Building ZINC001461383533 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461383533 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/650 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Br)cc3)CC2)cc1Cl) `ZINC001461383533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461383533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001461383533 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Br)cc3)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', 'Br', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 9, 12, 12, 12, 12, 24, 24, 21, 21, 24, 24, 12, 12, 6, 6, 6, 12, 12, 12, 6, 6, 12, 12, 12, 12, 24, 24, 24, 24, 12, 12, 12, 12, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/651 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Br)cc3)CC2)cc1Cl) `ZINC001461383533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461383533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001461383533 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Br)cc3)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', 'Br', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 9, 11, 11, 11, 11, 20, 20, 17, 17, 20, 20, 11, 11, 6, 6, 6, 11, 11, 11, 6, 6, 11, 11, 11, 11, 20, 20, 20, 20, 11, 11, 11, 11, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461383533 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533 Building ZINC001461383533 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461383533 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 650) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Br)cc3)CC2)cc1Cl) `ZINC001461383533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461383533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001461383533 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Br)cc3)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', 'Br', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 9, 12, 12, 12, 12, 24, 24, 21, 21, 24, 24, 12, 12, 6, 6, 6, 12, 12, 12, 6, 6, 12, 12, 12, 12, 24, 24, 24, 24, 12, 12, 12, 12, 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]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 651) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Br)cc3)CC2)cc1Cl) `ZINC001461383533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461383533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001461383533 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccc(Br)cc3)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', 'Br', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 17, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 4, 9, 11, 11, 11, 11, 20, 20, 17, 17, 20, 20, 11, 11, 6, 6, 6, 11, 11, 11, 6, 6, 11, 11, 11, 11, 20, 20, 20, 20, 11, 11, 11, 11, 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461383533 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461383533 Building ZINC001461486701 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461486701 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/652 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2ccnc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1) `ZINC001461486701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461486701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001461486701 none COc1ccc(c2ccnc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 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, 3, 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] 0 hydrogens 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, 7, 7, 29, 29, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 6, 6, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 29, 29] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/653 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1) `ZINC001461486701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461486701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001461486701 none COc1ccc(c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 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, 3, 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] 0 hydrogens 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, 7, 7, 30, 30, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 7, 30, 30, 30, 30, 30, 30, 30, 7, 7, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 30, 30] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461486701 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701 Building ZINC001461486701 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461486701 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 652) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc(c2ccnc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1) `ZINC001461486701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461486701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001461486701 none COc1ccc(c2ccnc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 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, 3, 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] 0 hydrogens 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, 7, 7, 29, 29, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 29, 29, 29, 29, 29, 29, 29, 6, 6, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 29, 29] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 653) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc(c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1) `ZINC001461486701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461486701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001461486701 none COc1ccc(c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 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, 3, 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] 0 hydrogens 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, 7, 7, 30, 30, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 7, 30, 30, 30, 30, 30, 30, 30, 7, 7, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 30, 30] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461486701 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461486701 Building ZINC001461570292 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461570292 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/654 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCO[C@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)C1) `ZINC001461570292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461570292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001461570292 none CC(C)(C)OC(=O)N1CCO[C@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 26, 39, 26, 26, 26, 26, 4, 26, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 3, 8, 8, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 8, 8, 2, 3, 3, 3, 3, 8, 8, 26, 26] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/655 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCO[C@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)C1) `ZINC001461570292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461570292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001461570292 none CC(C)(C)OC(=O)N1CCO[C@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 30, 41, 30, 30, 30, 30, 10, 30, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 10, 10, 3, 3, 3, 3, 3, 10, 10, 29, 30] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461570292 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292 Building ZINC001461570292 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461570292 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 654) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCO[C@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)C1) `ZINC001461570292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461570292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001461570292 none CC(C)(C)OC(=O)N1CCO[C@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 26, 39, 26, 26, 26, 26, 4, 26, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 3, 8, 8, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 8, 8, 2, 3, 3, 3, 3, 8, 8, 26, 26] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 655) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCO[C@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)C1) `ZINC001461570292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461570292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001461570292 none CC(C)(C)OC(=O)N1CCO[C@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 30, 41, 30, 30, 30, 30, 10, 30, 3, 10, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 10, 10, 3, 3, 3, 3, 3, 10, 10, 29, 30] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461570292 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570292 Building ZINC001461570295 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461570295 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/656 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCO[C@@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)C1) `ZINC001461570295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461570295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001461570295 none CC(C)(C)OC(=O)N1CCO[C@@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 24, 34, 24, 24, 24, 24, 9, 24, 4, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 11, 11, 2, 3, 3, 3, 3, 11, 11, 24, 24] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/657 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCO[C@@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)C1) `ZINC001461570295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461570295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001461570295 none CC(C)(C)OC(=O)N1CCO[C@@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 23, 33, 21, 22, 22, 20, 2, 20, 2, 12, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 22, 23, 12, 12, 2, 3, 3, 3, 3, 12, 12, 20, 20] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461570295 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295 Building ZINC001461570295 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461570295 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 656) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCO[C@@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)C1) `ZINC001461570295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461570295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001461570295 none CC(C)(C)OC(=O)N1CCO[C@@H](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(F)cc3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 24, 34, 24, 24, 24, 24, 9, 24, 4, 11, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 11, 11, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 24, 11, 11, 2, 3, 3, 3, 3, 11, 11, 24, 24] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 657) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCO[C@@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)C1) `ZINC001461570295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461570295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001461570295 none CC(C)(C)OC(=O)N1CCO[C@@H](c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(F)cc3)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 23, 33, 21, 22, 22, 20, 2, 20, 2, 12, 12, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 22, 23, 12, 12, 2, 3, 3, 3, 3, 12, 12, 20, 20] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461570295 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461570295 Building ZINC001461660368 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461660368 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/658 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1Cc2ccccc2O[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001461660368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461660368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001461660368 none O=C(N[C@@H]1Cc2ccccc2O[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 11, 11, 11, 11, 11, 6, 29, 29, 29, 29, 29, 29, 11, 11] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/659 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1Cc2ccccc2O[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001461660368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461660368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001461660368 none O=C(N[C@@H]1Cc2ccccc2O[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 12, 12, 12, 12, 12, 6, 29, 29, 29, 29, 29, 29, 12, 12] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461660368 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368 Building ZINC001461660368 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461660368 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 658) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1Cc2ccccc2O[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001461660368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461660368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001461660368 none O=C(N[C@@H]1Cc2ccccc2O[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 11, 11, 11, 11, 11, 6, 29, 29, 29, 29, 29, 29, 11, 11] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 659) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1Cc2ccccc2O[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001461660368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461660368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001461660368 none O=C(N[C@@H]1Cc2ccccc2O[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 12, 12, 12, 12, 12, 6, 29, 29, 29, 29, 29, 29, 12, 12] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461660368 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461660368 Building ZINC001461687391 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461687391 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/660 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(Cl)c(OC)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001461687391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461687391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001461687391 none CCOC(=O)c1ccc(Cl)c(OC)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 12, 5, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 16, 6, 16, 6, 6, 4, 6, 6, 6, 6, 11, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 6, 6, 11, 11, 11, 3, 7, 7, 7, 7, 7, 7, 7] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/661 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(Cl)c(OC)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001461687391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461687391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001461687391 none CCOC(=O)c1ccc(Cl)c(OC)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 12, 5, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 16, 6, 16, 6, 6, 4, 6, 6, 6, 6, 11, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 6, 6, 11, 11, 11, 3, 7, 7, 7, 7, 7, 7, 7] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461687391 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391 Building ZINC001461687391 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461687391 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 660) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1ccc(Cl)c(OC)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001461687391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461687391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001461687391 none CCOC(=O)c1ccc(Cl)c(OC)c1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 12, 5, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 16, 6, 16, 6, 6, 4, 6, 6, 6, 6, 11, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 6, 6, 11, 11, 11, 3, 7, 7, 7, 7, 7, 7, 7] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 661) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1ccc(Cl)c(OC)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001461687391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461687391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001461687391 none CCOC(=O)c1ccc(Cl)c(OC)c1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', '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, 5, 12, 1, 11, 1, 1, 1, 1, 16, 1, 12, 5, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 16, 6, 16, 6, 6, 4, 6, 6, 6, 6, 11, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 6, 6, 11, 11, 11, 3, 7, 7, 7, 7, 7, 7, 7] 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461687391 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461687391 Building ZINC001461800057 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461800057 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/662 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(S(=O)(=O)c2ccccc2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001461800057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461800057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001461800057 none O=C(Nc1cccc(S(=O)(=O)c2ccccc2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 2, 12, 12, 2, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 12, 12, 3, 21, 21, 21, 21, 21, 12, 6, 6, 6, 6, 6, 6, 6] 50 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, 42, 43, 44, 45, 46, 47]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/663 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(S(=O)(=O)c2ccccc2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001461800057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461800057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001461800057 none O=C(Nc1cccc(S(=O)(=O)c2ccccc2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 2, 12, 12, 8, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 12, 12, 12, 21, 21, 21, 21, 21, 12, 6, 6, 6, 6, 6, 6, 6] 50 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, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461800057 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057 Building ZINC001461800057 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001461800057 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 662) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1cccc(S(=O)(=O)c2ccccc2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001461800057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001461800057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001461800057 none O=C(Nc1cccc(S(=O)(=O)c2ccccc2)c1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 2, 12, 12, 2, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 12, 12, 3, 21, 21, 21, 21, 21, 12, 6, 6, 6, 6, 6, 6, 6] 50 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, 42, 43, 44, 45, 46, 47]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 663) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1cccc(S(=O)(=O)c2ccccc2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC001461800057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001461800057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001461800057 none O=C(Nc1cccc(S(=O)(=O)c2ccccc2)c1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 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, 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: [2, 1, 2, 2, 12, 12, 8, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 12, 12, 12, 21, 21, 21, 21, 21, 12, 6, 6, 6, 6, 6, 6, 6] 50 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, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001461800057 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001461800057 Building ZINC001462060214 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462060214 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/664 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nn(c2ncccc2Cl)cc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001462060214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462060214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001462060214 none O=C(Nc1nn(c2ncccc2Cl)cc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 29, 29, 29, 29, 29, 29, 17, 17, 17, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 4, 29, 29, 29, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/665 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1nn(c2ncccc2Cl)cc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001462060214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462060214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001462060214 none O=C(Nc1nn(c2ncccc2Cl)cc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 30, 30, 30, 30, 30, 30, 16, 16, 16, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 4, 30, 30, 30, 16, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462060214 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214 Building ZINC001462060214 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462060214 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 664) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1nn(c2ncccc2Cl)cc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001462060214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462060214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001462060214 none O=C(Nc1nn(c2ncccc2Cl)cc1Br)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 29, 29, 29, 29, 29, 29, 17, 17, 17, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 4, 29, 29, 29, 17, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 665) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1nn(c2ncccc2Cl)cc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001462060214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462060214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001462060214 none O=C(Nc1nn(c2ncccc2Cl)cc1Br)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'Br', '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'] dock atom type numbers: [11, 1, 8, 1, 8, 8, 1, 8, 1, 1, 1, 1, 16, 1, 1, 17, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need 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, 16, 16, 16, 30, 30, 30, 30, 30, 30, 16, 16, 16, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 4, 30, 30, 30, 16, 8, 8, 8, 8, 8, 8, 8, 8, 8] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462060214 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462060214 Building ZINC001462068482 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462068482 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/666 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2nc3ccccc3s2)n1) `ZINC001462068482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462068482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001462068482 none Cc1csc(CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2nc3ccccc3s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.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.3', 'C.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', '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, 1, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 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, 44, 45, 46, 47]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/667 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2nc3ccccc3s2)n1) `ZINC001462068482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462068482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001462068482 none Cc1csc(CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2nc3ccccc3s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.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.3', 'C.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', '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, 1, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 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, 44, 45, 46, 47]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462068482 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482 Building ZINC001462068482 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462068482 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 666) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1csc(CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2nc3ccccc3s2)n1) `ZINC001462068482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462068482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001462068482 none Cc1csc(CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2nc3ccccc3s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.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.3', 'C.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', '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, 1, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 18, 18, 18, 18, 18, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 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, 44, 45, 46, 47]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 667) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1csc(CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2nc3ccccc3s2)n1) `ZINC001462068482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462068482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001462068482 none Cc1csc(CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2nc3ccccc3s2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.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.3', 'C.2', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', '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, 1, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 19, 19, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 12, 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, 44, 45, 46, 47]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462068482 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462068482 Building ZINC001462194956 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462194956 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/668 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1ccc2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CCO2) `ZINC001462194956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462194956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001462194956 none CC(C)(C)OC(=O)NCc1ccc2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 33, 47, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 10, 10, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [45, 46, 47, 48, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/669 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1ccc2c(c1)N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CCO2) `ZINC001462194956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462194956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001462194956 none CC(C)(C)OC(=O)NCc1ccc2c(c1)N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 32, 45, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 10, 10, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [45, 46, 47, 48, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/6899/xaj-8058088.10/working/building/ZINC001462194956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462194956 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956 Building ZINC001462194956 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462194956 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 668) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NCc1ccc2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CCO2) `ZINC001462194956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462194956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001462194956 none CC(C)(C)OC(=O)NCc1ccc2c(c1)N(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 33, 47, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 10, 10, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [45, 46, 47, 48, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 669) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NCc1ccc2c(c1)N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CCO2) `ZINC001462194956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462194956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001462194956 none CC(C)(C)OC(=O)NCc1ccc2c(c1)N(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 32, 45, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 10, 10, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [45, 46, 47, 48, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/6899/xaj-8058088.10/working/building/ZINC001462194956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462194956 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462194956 Building ZINC001462205834 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462205834 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/670 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/670' -> `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)Nc1c(Cl)n(C)nc1C(F)(F)F) `ZINC001462205834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462205834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001462205834 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(Cl)n(C)nc1C(F)(F)F 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.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', '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, 1, 1, 16, 8, 5, 8, 1, 5, 15, 15, 15, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 7, 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]) total number of confs: 71 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/671 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/671' -> `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)Nc1c(Cl)n(C)nc1C(F)(F)F) `ZINC001462205834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462205834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001462205834 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(Cl)n(C)nc1C(F)(F)F 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.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', '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, 1, 1, 16, 8, 5, 8, 1, 5, 15, 15, 15, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 7, 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]) total number of confs: 71 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462205834 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834 Building ZINC001462205834 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462205834 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 670) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(Cl)n(C)nc1C(F)(F)F) `ZINC001462205834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462205834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001462205834 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1c(Cl)n(C)nc1C(F)(F)F 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.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', '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, 1, 1, 16, 8, 5, 8, 1, 5, 15, 15, 15, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 7, 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]) total number of confs: 71 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 671) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(Cl)n(C)nc1C(F)(F)F) `ZINC001462205834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462205834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001462205834 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1c(Cl)n(C)nc1C(F)(F)F 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.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', '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, 1, 1, 16, 8, 5, 8, 1, 5, 15, 15, 15, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 7, 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]) total number of confs: 71 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462205834 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462205834 Building ZINC001462258686 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462258686 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/672 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(I)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c1) `ZINC001462258686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462258686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462258686 none CCOC(=O)c1ccc(I)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 18, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 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] 0 hydrogens need 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, 42, 10, 42, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 50, 50, 50, 50, 50, 10, 10, 4, 3, 3, 3, 3, 3, 3, 3, 10] 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: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/673 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/673' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccc(I)c(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c1) `ZINC001462258686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462258686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462258686 none CCOC(=O)c1ccc(I)c(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 18, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 41, 10, 41, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 10, 50, 50, 50, 50, 50, 10, 10, 4, 3, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462258686 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686 Building ZINC001462258686 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462258686 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 672) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1ccc(I)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c1) `ZINC001462258686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462258686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462258686 none CCOC(=O)c1ccc(I)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 18, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 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] 0 hydrogens need 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, 42, 10, 42, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 50, 50, 50, 50, 50, 10, 10, 4, 3, 3, 3, 3, 3, 3, 3, 10] 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: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 673) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1ccc(I)c(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c1) `ZINC001462258686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462258686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462258686 none CCOC(=O)c1ccc(I)c(NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 18, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 1, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 41, 10, 41, 10, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 10, 50, 50, 50, 50, 50, 10, 10, 4, 3, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462258686 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462258686 Building ZINC001462270633 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462270633 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/674 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1[nH]c2ccccc2c1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001462270633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462270633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001462270633 none CCOC(=O)c1[nH]c2ccccc2c1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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, 5, 12, 1, 11, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 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, 7, 3, 7, 5, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 25, 19, 8, 19, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 34, 34, 34, 34, 34, 8, 8, 8, 8, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/675 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1[nH]c2ccccc2c1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001462270633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462270633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001462270633 none CCOC(=O)c1[nH]c2ccccc2c1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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, 5, 12, 1, 11, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 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, 7, 3, 7, 5, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 22, 8, 22, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 40, 40, 40, 40, 40, 8, 8, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462270633 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633 Building ZINC001462270633 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462270633 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 674) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1[nH]c2ccccc2c1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001462270633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462270633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001462270633 none CCOC(=O)c1[nH]c2ccccc2c1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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, 5, 12, 1, 11, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 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, 7, 3, 7, 5, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 25, 19, 8, 19, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 34, 34, 34, 34, 34, 8, 8, 8, 8, 2, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 675) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1[nH]c2ccccc2c1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001462270633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462270633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001462270633 none CCOC(=O)c1[nH]c2ccccc2c1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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, 5, 12, 1, 11, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 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, 7, 3, 7, 5, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 22, 8, 22, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 40, 40, 40, 40, 40, 8, 8, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462270633 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462270633 Building ZINC001462313420 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462313420 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/676 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC001462313420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462313420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001462313420 none CC(C)(C)OC(=O)NC[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 21, 33, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 21, 10, 10, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4] 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/677 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC001462313420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462313420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001462313420 none CC(C)(C)OC(=O)NC[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 7] 0 hydrogens 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, 23, 31, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 1, 1, 1, 3, 3, 3, 3, 7, 7, 7, 3, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 23, 9, 9, 4, 4, 4, 4, 4, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 4] 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462313420 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420 Building ZINC001462313420 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462313420 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 676) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/676: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC001462313420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462313420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001462313420 none CC(C)(C)OC(=O)NC[C@@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 21, 33, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 21, 10, 10, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4] 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 677) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC001462313420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462313420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001462313420 none CC(C)(C)OC(=O)NC[C@@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 7] 0 hydrogens 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, 23, 31, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 1, 1, 1, 3, 3, 3, 3, 7, 7, 7, 3, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 23, 9, 9, 4, 4, 4, 4, 4, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 4] 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462313420 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313420 Building ZINC001462313423 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462313423 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/678 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC001462313423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462313423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001462313423 none CC(C)(C)OC(=O)NC[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 7] 0 hydrogens 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, 22, 31, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 3, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 22, 9, 9, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 4, 4] 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/679 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC001462313423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462313423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001462313423 none CC(C)(C)OC(=O)NC[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 7] 0 hydrogens 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, 19, 31, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 19, 10, 10, 4, 4, 4, 4, 4, 4, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 4, 4] 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462313423 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423 Building ZINC001462313423 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462313423 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 678) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC001462313423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462313423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001462313423 none CC(C)(C)OC(=O)NC[C@H]1Cc2ccccc2N(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 7] 0 hydrogens 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, 22, 31, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 1, 1, 1, 3, 3, 3, 3, 6, 6, 6, 3, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 22, 9, 9, 4, 4, 4, 4, 4, 4, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 4, 4] 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 679) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC001462313423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462313423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001462313423 none CC(C)(C)OC(=O)NC[C@H]1Cc2ccccc2N(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 7] 0 hydrogens 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, 19, 31, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 19, 10, 10, 4, 4, 4, 4, 4, 4, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 4, 4] 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462313423 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462313423 Building ZINC001462360372 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001462360372 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/680 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)CC1) `ZINC001462360372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462360372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462360372 none CC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)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', '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.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 7, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 43, 43, 43, 43] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 88 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/681 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)CC1) `ZINC001462360372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462360372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462360372 none CC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)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', '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.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 38, 7, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 42, 42, 42, 42] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 87 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/682 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/682' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)CC1) `ZINC001462360372.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001462360372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462360372 none CC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)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', '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.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 38, 7, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 42, 42, 42, 42] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 87 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/683 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/683' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)CC1) `ZINC001462360372.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001462360372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462360372 none CC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)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', '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.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 38, 7, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 42, 42, 42, 42] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 87 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462360372 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 Building ZINC001462360372 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001462360372 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 680) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)CC1) `ZINC001462360372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462360372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462360372 none CC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)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', '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.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 7, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 43, 43, 43, 43] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 88 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 681) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)CC1) `ZINC001462360372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462360372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462360372 none CC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)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', '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.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 38, 7, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 42, 42, 42, 42] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 87 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 682) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/682: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)CC1) `ZINC001462360372.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001462360372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462360372 none CC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)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', '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.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 38, 7, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 42, 42, 42, 42] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 87 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 683) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/683: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)CC1) `ZINC001462360372.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001462360372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462360372 none CC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)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', '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.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 38, 7, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 42, 42, 42, 42] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 87 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462360372 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 Building ZINC001462360372 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001462360372 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 680) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)CC1) `ZINC001462360372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462360372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462360372 none CC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)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', '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.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 7, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 43, 43, 43, 43] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 88 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 681) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)CC1) `ZINC001462360372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462360372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462360372 none CC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)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', '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.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 38, 7, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 42, 42, 42, 42] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 87 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 682) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/682: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)CC1) `ZINC001462360372.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001462360372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462360372 none CC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)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', '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.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 38, 7, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 42, 42, 42, 42] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 87 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 683) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/683: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)CC1) `ZINC001462360372.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001462360372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462360372 none CC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)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', '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.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 38, 7, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 42, 42, 42, 42] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 87 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462360372 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 Building ZINC001462360372 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001462360372 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 680) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)CC1) `ZINC001462360372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462360372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462360372 none CC[N@]1CC[N@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)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', '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.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 7, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 43, 43, 43, 43] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 88 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 681) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)CC1) `ZINC001462360372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462360372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462360372 none CC[N@]1CC[N@@](c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)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', '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.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 38, 7, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 42, 42, 42, 42] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 87 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 682) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/682: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)CC1) `ZINC001462360372.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001462360372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462360372 none CC[N@]1CC[N@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)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', '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.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 38, 7, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 42, 42, 42, 42] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 87 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 683) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/683: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)CC1) `ZINC001462360372.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001462360372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001462360372 none CC[N@]1CC[N@@](c2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)cc2F)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', '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.ar', 'C.ar', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 38, 7, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 42, 42, 42, 42] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 87 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462360372 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462360372 Building ZINC001462361502 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462361502 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/684 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC)c2sc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)nc21) `ZINC001462361502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462361502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462361502 none COc1ccc(OC)c2sc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.3', 'C.2', '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', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 8, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 4, 9, 9, 9, 4, 4, 8, 8, 8, 2, 4, 4, 4, 8, 8, 4, 8, 8, 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/685 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC)c2sc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)nc21) `ZINC001462361502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462361502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462361502 none COc1ccc(OC)c2sc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.3', 'C.2', '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', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 9, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 4, 9, 9, 9, 4, 4, 9, 9, 9, 2, 4, 4, 4, 8, 8, 8, 8, 8, 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462361502 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502 Building ZINC001462361502 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462361502 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 684) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc(OC)c2sc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)nc21) `ZINC001462361502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462361502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462361502 none COc1ccc(OC)c2sc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.3', 'C.2', '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', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 8, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 4, 9, 9, 9, 4, 4, 8, 8, 8, 2, 4, 4, 4, 8, 8, 4, 8, 8, 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]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 685) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc(OC)c2sc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)nc21) `ZINC001462361502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462361502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462361502 none COc1ccc(OC)c2sc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)nc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.3', 'C.2', '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', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 9, 4, 4, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 6, 8, 8, 4, 4, 4, 4, 9, 9, 9, 4, 4, 9, 9, 9, 2, 4, 4, 4, 8, 8, 8, 8, 8, 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462361502 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462361502 Building ZINC001462459841 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462459841 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/686 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2ccc(Br)cc2)cn1) `ZINC001462459841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462459841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001462459841 none Cn1cc(CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2ccc(Br)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 4, 8, 8, 6, 8, 8, 8, 25, 25, 25, 25, 25, 25, 10, 10, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 8, 8, 8, 8, 25] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/687 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2ccc(Br)cc2)cn1) `ZINC001462459841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462459841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001462459841 none Cn1cc(CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2ccc(Br)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 5, 10, 10, 5, 5, 10, 10, 24, 24, 24, 24, 24, 24, 10, 10, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 10, 10, 10, 10, 24] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462459841 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841 Building ZINC001462459841 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462459841 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 686) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cn1cc(CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2ccc(Br)cc2)cn1) `ZINC001462459841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462459841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001462459841 none Cn1cc(CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2ccc(Br)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 4, 8, 8, 6, 8, 8, 8, 25, 25, 25, 25, 25, 25, 10, 10, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 8, 8, 8, 8, 25] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 687) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cn1cc(CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2ccc(Br)cc2)cn1) `ZINC001462459841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462459841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001462459841 none Cn1cc(CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c2ccc(Br)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 5, 10, 10, 5, 5, 10, 10, 24, 24, 24, 24, 24, 24, 10, 10, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 10, 10, 10, 10, 24] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462459841 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462459841 Building ZINC001462600691 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462600691 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/688 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)(C)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001462600691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462600691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001462600691 none COCC(C)(C)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 11, 11, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 2, 2, 2, 2, 8, 8, 2, 8, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/689 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)(C)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001462600691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462600691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001462600691 none COCC(C)(C)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 11, 11, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 2, 2, 2, 2, 8, 8, 2, 8, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462600691 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691 Building ZINC001462600691 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462600691 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 688) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COCC(C)(C)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001462600691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462600691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001462600691 none COCC(C)(C)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 11, 11, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 2, 2, 2, 2, 8, 8, 2, 8, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 689) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COCC(C)(C)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC001462600691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462600691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001462600691 none COCC(C)(C)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 12, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 11, 11, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 2, 2, 2, 2, 8, 8, 2, 8, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462600691 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462600691 Building ZINC001462632754 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462632754 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/690 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](C[C@@H](NC(=O)OC(C)(C)C)C3CCCC3)C2)cn1) `ZINC001462632754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462632754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001462632754 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](C[C@@H](NC(=O)OC(C)(C)C)C3CCCC3)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 9, 14, 14, 20, 28, 28, 28, 28, 28, 28, 14, 18, 18, 18, 18, 5, 3, 3, 7, 7, 7, 7, 7, 3, 5, 5, 5, 5, 5, 5, 9, 9, 20, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/691 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](C[C@@H](NC(=O)OC(C)(C)C)C3CCCC3)C2)cn1) `ZINC001462632754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462632754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001462632754 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](C[C@@H](NC(=O)OC(C)(C)C)C3CCCC3)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 6, 6, 6, 6, 6, 6, 6, 8, 11, 11, 16, 22, 22, 22, 22, 22, 22, 11, 17, 17, 17, 17, 6, 5, 5, 10, 10, 10, 10, 10, 5, 6, 6, 6, 6, 6, 6, 8, 8, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 5] 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462632754 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754 Building ZINC001462632754 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462632754 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 690) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](C[C@@H](NC(=O)OC(C)(C)C)C3CCCC3)C2)cn1) `ZINC001462632754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462632754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001462632754 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](C[C@@H](NC(=O)OC(C)(C)C)C3CCCC3)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5, 9, 14, 14, 20, 28, 28, 28, 28, 28, 28, 14, 18, 18, 18, 18, 5, 3, 3, 7, 7, 7, 7, 7, 3, 5, 5, 5, 5, 5, 5, 9, 9, 20, 28, 28, 28, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 691) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](C[C@@H](NC(=O)OC(C)(C)C)C3CCCC3)C2)cn1) `ZINC001462632754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462632754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001462632754 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](C[C@@H](NC(=O)OC(C)(C)C)C3CCCC3)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 6, 6, 6, 6, 6, 6, 6, 8, 11, 11, 16, 22, 22, 22, 22, 22, 22, 11, 17, 17, 17, 17, 6, 5, 5, 10, 10, 10, 10, 10, 5, 6, 6, 6, 6, 6, 6, 8, 8, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 5] 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462632754 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632754 Building ZINC001462632762 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462632762 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/692 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](C[C@H](NC(=O)OC(C)(C)C)C3CCCC3)C2)cn1) `ZINC001462632762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462632762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001462632762 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](C[C@H](NC(=O)OC(C)(C)C)C3CCCC3)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 6, 8, 8, 14, 21, 21, 23, 23, 23, 23, 9, 14, 14, 14, 14, 3, 3, 3, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 6, 6, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/693 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](C[C@H](NC(=O)OC(C)(C)C)C3CCCC3)C2)cn1) `ZINC001462632762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462632762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001462632762 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](C[C@H](NC(=O)OC(C)(C)C)C3CCCC3)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 6, 9, 9, 13, 21, 21, 22, 22, 22, 22, 9, 15, 15, 15, 15, 3, 4, 4, 7, 7, 7, 7, 7, 4, 3, 3, 3, 3, 3, 3, 6, 6, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462632762 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762 Building ZINC001462632762 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462632762 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 692) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/692: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](C[C@H](NC(=O)OC(C)(C)C)C3CCCC3)C2)cn1) `ZINC001462632762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462632762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001462632762 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](C[C@H](NC(=O)OC(C)(C)C)C3CCCC3)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 6, 8, 8, 14, 21, 21, 23, 23, 23, 23, 9, 14, 14, 14, 14, 3, 3, 3, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 6, 6, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 693) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/693: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](C[C@H](NC(=O)OC(C)(C)C)C3CCCC3)C2)cn1) `ZINC001462632762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462632762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001462632762 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](C[C@H](NC(=O)OC(C)(C)C)C3CCCC3)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 4, 4, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 6, 9, 9, 13, 21, 21, 22, 22, 22, 22, 9, 15, 15, 15, 15, 3, 4, 4, 7, 7, 7, 7, 7, 4, 3, 3, 3, 3, 3, 3, 6, 6, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462632762 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632762 Building ZINC001462632770 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462632770 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/694 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](C[C@H](NC(=O)OC(C)(C)C)C3CCCC3)C2)cn1) `ZINC001462632770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462632770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001462632770 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](C[C@H](NC(=O)OC(C)(C)C)C3CCCC3)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 6, 6, 6, 6, 6, 6, 6, 8, 12, 12, 17, 23, 23, 23, 23, 23, 23, 12, 19, 19, 19, 19, 6, 4, 4, 8, 8, 8, 8, 8, 4, 6, 6, 6, 6, 6, 6, 8, 8, 17, 23, 23, 23, 23, 23, 23, 23, 23, 23, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 4] 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/695 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](C[C@H](NC(=O)OC(C)(C)C)C3CCCC3)C2)cn1) `ZINC001462632770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462632770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001462632770 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](C[C@H](NC(=O)OC(C)(C)C)C3CCCC3)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 7, 12, 12, 18, 27, 27, 27, 27, 27, 27, 12, 19, 19, 19, 19, 4, 3, 3, 7, 7, 7, 7, 7, 3, 4, 4, 4, 4, 4, 4, 7, 7, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462632770 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770 Building ZINC001462632770 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462632770 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 694) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](C[C@H](NC(=O)OC(C)(C)C)C3CCCC3)C2)cn1) `ZINC001462632770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462632770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001462632770 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](C[C@H](NC(=O)OC(C)(C)C)C3CCCC3)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 6, 6, 6, 6, 6, 6, 6, 8, 12, 12, 17, 23, 23, 23, 23, 23, 23, 12, 19, 19, 19, 19, 6, 4, 4, 8, 8, 8, 8, 8, 4, 6, 6, 6, 6, 6, 6, 8, 8, 17, 23, 23, 23, 23, 23, 23, 23, 23, 23, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 4] 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 695) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](C[C@H](NC(=O)OC(C)(C)C)C3CCCC3)C2)cn1) `ZINC001462632770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462632770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001462632770 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](C[C@H](NC(=O)OC(C)(C)C)C3CCCC3)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 7, 12, 12, 18, 27, 27, 27, 27, 27, 27, 12, 19, 19, 19, 19, 4, 3, 3, 7, 7, 7, 7, 7, 3, 4, 4, 4, 4, 4, 4, 7, 7, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462632770 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632770 Building ZINC001462632778 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462632778 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/696 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](C[C@@H](NC(=O)OC(C)(C)C)C3CCCC3)C2)cn1) `ZINC001462632778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462632778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001462632778 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](C[C@@H](NC(=O)OC(C)(C)C)C3CCCC3)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 3, 3, 3, 6, 9, 9, 13, 20, 20, 23, 23, 23, 23, 9, 15, 15, 15, 15, 3, 4, 4, 9, 9, 9, 9, 9, 4, 3, 3, 3, 3, 3, 3, 6, 6, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/697 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](C[C@@H](NC(=O)OC(C)(C)C)C3CCCC3)C2)cn1) `ZINC001462632778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462632778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001462632778 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](C[C@@H](NC(=O)OC(C)(C)C)C3CCCC3)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 6, 8, 8, 13, 18, 18, 23, 24, 24, 24, 8, 14, 14, 14, 14, 3, 3, 3, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 6, 6, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462632778 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778 Building ZINC001462632778 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462632778 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 696) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](C[C@@H](NC(=O)OC(C)(C)C)C3CCCC3)C2)cn1) `ZINC001462632778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462632778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001462632778 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](C[C@@H](NC(=O)OC(C)(C)C)C3CCCC3)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 3, 3, 3, 3, 6, 9, 9, 13, 20, 20, 23, 23, 23, 23, 9, 15, 15, 15, 15, 3, 4, 4, 9, 9, 9, 9, 9, 4, 3, 3, 3, 3, 3, 3, 6, 6, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 15, 15, 15, 15, 15, 15, 15, 15, 15, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 697) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](C[C@@H](NC(=O)OC(C)(C)C)C3CCCC3)C2)cn1) `ZINC001462632778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462632778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001462632778 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](C[C@@H](NC(=O)OC(C)(C)C)C3CCCC3)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', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', '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, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 6, 8, 8, 13, 18, 18, 23, 24, 24, 24, 8, 14, 14, 14, 14, 3, 3, 3, 7, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 6, 6, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 14, 14, 14, 14, 14, 14, 14, 14, 14, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462632778 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462632778 Building ZINC001462644956 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462644956 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/698 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)(C(F)(F)F)CC1) `ZINC001462644956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462644956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001462644956 none CC(C)(C)OC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 18, 12, 18, 12, 12, 12, 7, 4, 1, 4, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/699 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)(C(F)(F)F)CC1) `ZINC001462644956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462644956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001462644956 none CC(C)(C)OC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 17, 12, 17, 12, 12, 12, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462644956 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956 Building ZINC001462644956 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462644956 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 698) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)(C(F)(F)F)CC1) `ZINC001462644956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462644956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001462644956 none CC(C)(C)OC(=O)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 18, 12, 18, 12, 12, 12, 7, 4, 1, 4, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 12, 12, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 699) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)(C(F)(F)F)CC1) `ZINC001462644956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462644956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001462644956 none CC(C)(C)OC(=O)N1CCC(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)(C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 17, 12, 17, 12, 12, 12, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462644956 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462644956 Building ZINC001462707346 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462707346 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/700 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/700' -> `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)Nc1nc2cccc(Br)c2[nH]1) `ZINC001462707346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462707346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001462707346 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2cccc(Br)c2[nH]1 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', '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, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 13, 13, 5, 13, 13, 5, 5, 1, 1, 1, 1, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 13, 13, 5, 13, 13, 5, 5, 5, 10, 11, 11, 11] 23 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]) total number of confs: 59 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/701 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/701' -> `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)Nc1nc2cccc(Br)c2[nH]1) `ZINC001462707346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462707346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001462707346 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2cccc(Br)c2[nH]1 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', '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, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 13, 13, 5, 13, 13, 5, 5, 1, 1, 1, 1, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 13, 13, 9, 13, 13, 5, 5, 5, 10, 11, 11, 11] 23 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]) total number of confs: 67 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462707346 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346 Building ZINC001462707346 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462707346 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 700) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2cccc(Br)c2[nH]1) `ZINC001462707346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462707346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001462707346 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2cccc(Br)c2[nH]1 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', '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, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 13, 13, 5, 13, 13, 5, 5, 1, 1, 1, 1, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 13, 13, 5, 13, 13, 5, 5, 5, 10, 11, 11, 11] 23 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]) total number of confs: 59 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 701) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2cccc(Br)c2[nH]1) `ZINC001462707346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462707346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001462707346 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2cccc(Br)c2[nH]1 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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', '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, 1, 8, 1, 1, 1, 1, 1, 17, 1, 8, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 5, 5, 5, 5, 13, 13, 5, 13, 13, 5, 5, 1, 1, 1, 1, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 13, 13, 9, 13, 13, 5, 5, 5, 10, 11, 11, 11] 23 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]) total number of confs: 67 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462707346 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462707346 Building ZINC001462757218 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462757218 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/702 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc2c(s1)CCC2) `ZINC001462757218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462757218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001462757218 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc2c(s1)CCC2 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 14, 5, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/703 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc2c(s1)CCC2) `ZINC001462757218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462757218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001462757218 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc2c(s1)CCC2 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 14, 5, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462757218 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218 Building ZINC001462757218 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462757218 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 702) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc2c(s1)CCC2) `ZINC001462757218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462757218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001462757218 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc2c(s1)CCC2 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 14, 5, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 11, 11, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 703) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc2c(s1)CCC2) `ZINC001462757218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462757218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001462757218 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc2c(s1)CCC2 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 14, 5, 5, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462757218 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462757218 Building ZINC001462820603 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462820603 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/704 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F) `ZINC001462820603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462820603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462820603 none CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 23, 36, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 2, 2, 2, 2, 10, 10, 10, 10] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/705 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F) `ZINC001462820603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462820603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462820603 none CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 25, 38, 13, 13, 13, 13, 8, 2, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 13, 13, 2, 2, 2, 2, 13, 13, 13, 13] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462820603 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603 Building ZINC001462820603 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462820603 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 704) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F) `ZINC001462820603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462820603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462820603 none CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 23, 36, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 2, 2, 2, 2, 10, 10, 10, 10] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 705) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F) `ZINC001462820603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462820603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462820603 none CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 25, 38, 13, 13, 13, 13, 8, 2, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 13, 13, 2, 2, 2, 2, 13, 13, 13, 13] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462820603 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820603 Building ZINC001462820604 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462820604 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/706 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F) `ZINC001462820604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462820604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462820604 none CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 24, 37, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 10, 10, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [44, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/707 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F) `ZINC001462820604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462820604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462820604 none CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 26, 36, 14, 14, 14, 14, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 14, 14, 1, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [44, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50]) total number of confs: 138 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462820604 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604 Building ZINC001462820604 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462820604 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 706) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F) `ZINC001462820604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462820604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462820604 none CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 24, 37, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 10, 10, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [44, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 707) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F) `ZINC001462820604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462820604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462820604 none CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 26, 36, 14, 14, 14, 14, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 14, 14, 1, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [44, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50]) total number of confs: 138 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462820604 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820604 Building ZINC001462820605 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462820605 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/708 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F) `ZINC001462820605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462820605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462820605 none CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 27, 41, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 11, 11, 2, 2, 2, 2, 11, 11, 11, 11] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/709 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F) `ZINC001462820605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462820605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462820605 none CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 29, 44, 14, 14, 14, 14, 11, 1, 11, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 14, 14, 2, 2, 2, 2, 14, 14, 14, 14] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462820605 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605 Building ZINC001462820605 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462820605 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 708) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F) `ZINC001462820605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462820605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462820605 none CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 27, 41, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 11, 11, 2, 2, 2, 2, 11, 11, 11, 11] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 709) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F) `ZINC001462820605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462820605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462820605 none CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 29, 44, 14, 14, 14, 14, 11, 1, 11, 1, 1, 1, 2, 2, 1, 1, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 14, 14, 2, 2, 2, 2, 14, 14, 14, 14] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462820605 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820605 Building ZINC001462820606 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462820606 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/710 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F) `ZINC001462820606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462820606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462820606 none CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 28, 40, 12, 12, 12, 12, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/711 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F) `ZINC001462820606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462820606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462820606 none CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 24, 37, 9, 9, 9, 9, 6, 2, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 9, 9, 2, 2, 2, 2, 9, 9, 9, 9] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462820606 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606 Building ZINC001462820606 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462820606 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 710) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F) `ZINC001462820606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462820606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462820606 none CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 28, 40, 12, 12, 12, 12, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 711) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F) `ZINC001462820606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462820606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001462820606 none CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 24, 37, 9, 9, 9, 9, 6, 2, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 9, 9, 2, 2, 2, 2, 9, 9, 9, 9] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462820606 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462820606 Building ZINC001462829693 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462829693 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/712 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@H]1C(F)(F)F) `ZINC001462829693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462829693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462829693 none CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 40, 40, 30, 19, 30, 10, 10, 10, 10, 6, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 40, 40, 40, 40, 40, 40, 40, 40, 40, 19, 10, 10, 2, 2, 10, 10, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/713 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@H]1C(F)(F)F) `ZINC001462829693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462829693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462829693 none CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 29, 19, 29, 8, 8, 8, 8, 5, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 19, 8, 8, 4, 4, 8, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462829693 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693 Building ZINC001462829693 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462829693 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 712) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@H]1C(F)(F)F) `ZINC001462829693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462829693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462829693 none CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 40, 40, 30, 19, 30, 10, 10, 10, 10, 6, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 40, 40, 40, 40, 40, 40, 40, 40, 40, 19, 10, 10, 2, 2, 10, 10, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 713) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@H]1C(F)(F)F) `ZINC001462829693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462829693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462829693 none CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 29, 19, 29, 8, 8, 8, 8, 5, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 19, 8, 8, 4, 4, 8, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462829693 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829693 Building ZINC001462829698 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462829698 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/714 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@@H]1C(F)(F)F) `ZINC001462829698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462829698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462829698 none CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 26, 17, 26, 8, 8, 8, 8, 5, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 36, 36, 36, 36, 36, 36, 36, 36, 36, 17, 8, 8, 4, 4, 8, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/715 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@@H]1C(F)(F)F) `ZINC001462829698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462829698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462829698 none CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 32, 23, 32, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 23, 11, 11, 2, 2, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462829698 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698 Building ZINC001462829698 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462829698 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 714) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@@H]1C(F)(F)F) `ZINC001462829698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462829698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462829698 none CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 26, 17, 26, 8, 8, 8, 8, 5, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 36, 36, 36, 36, 36, 36, 36, 36, 36, 17, 8, 8, 4, 4, 8, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 715) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@@H]1C(F)(F)F) `ZINC001462829698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462829698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462829698 none CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 32, 23, 32, 11, 11, 11, 11, 8, 2, 8, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 23, 11, 11, 2, 2, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462829698 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829698 Building ZINC001462829705 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462829705 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/716 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@@H]1C(F)(F)F) `ZINC001462829705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462829705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462829705 none CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 18, 28, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 32, 18, 10, 10, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/717 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@@H]1C(F)(F)F) `ZINC001462829705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462829705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462829705 none CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 19, 28, 12, 12, 12, 12, 10, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 12, 12, 3, 3, 12, 12, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462829705 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705 Building ZINC001462829705 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462829705 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 716) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@@H]1C(F)(F)F) `ZINC001462829705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462829705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462829705 none CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 18, 28, 10, 10, 10, 10, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 32, 32, 32, 32, 32, 32, 32, 32, 32, 18, 10, 10, 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 717) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@@H]1C(F)(F)F) `ZINC001462829705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462829705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462829705 none CC(C)(C)OC(=O)N[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 19, 28, 12, 12, 12, 12, 10, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 12, 12, 3, 3, 12, 12, 12, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462829705 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829705 Building ZINC001462829709 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462829709 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/718 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@H]1C(F)(F)F) `ZINC001462829709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462829709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462829709 none CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 20, 30, 10, 10, 10, 10, 7, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 10, 10, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/719 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@H]1C(F)(F)F) `ZINC001462829709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462829709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462829709 none CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 27, 17, 27, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 36, 36, 36, 36, 36, 36, 36, 36, 36, 17, 8, 8, 3, 3, 8, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462829709 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709 Building ZINC001462829709 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462829709 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 718) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@H]1C(F)(F)F) `ZINC001462829709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462829709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462829709 none CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 20, 30, 10, 10, 10, 10, 7, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 10, 10, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 719) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@H]1C(F)(F)F) `ZINC001462829709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462829709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001462829709 none CC(C)(C)OC(=O)N[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 27, 17, 27, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 36, 36, 36, 36, 36, 36, 36, 36, 36, 17, 8, 8, 3, 3, 8, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462829709 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462829709 Building ZINC001462847290 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462847290 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/720 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1Oc1ccc(Br)cc1F)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001462847290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462847290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001462847290 none CN(Cc1ccccc1Oc1ccc(Br)cc1F)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 15, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 11, 11, 11, 11, 11, 11, 24, 35, 35, 35, 35, 35, 35, 35, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 7, 7, 11, 11, 11, 11, 35, 35, 35, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/721 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1ccccc1Oc1ccc(Br)cc1F)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001462847290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462847290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001462847290 none CN(Cc1ccccc1Oc1ccc(Br)cc1F)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 15, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 11, 11, 9, 11, 11, 11, 24, 35, 35, 35, 35, 35, 35, 35, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 7, 7, 11, 11, 11, 11, 35, 35, 35, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462847290 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290 Building ZINC001462847290 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462847290 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 720) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(Cc1ccccc1Oc1ccc(Br)cc1F)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001462847290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462847290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001462847290 none CN(Cc1ccccc1Oc1ccc(Br)cc1F)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 15, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 11, 11, 11, 11, 11, 11, 24, 35, 35, 35, 35, 35, 35, 35, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 7, 7, 11, 11, 11, 11, 35, 35, 35, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 721) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(Cc1ccccc1Oc1ccc(Br)cc1F)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001462847290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462847290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001462847290 none CN(Cc1ccccc1Oc1ccc(Br)cc1F)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 17, 1, 1, 15, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 11, 11, 9, 11, 11, 11, 24, 35, 35, 35, 35, 35, 35, 35, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 7, 7, 11, 11, 11, 11, 35, 35, 35, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462847290 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462847290 Building ZINC001462850841 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462850841 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/722 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/722' -> `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]1CC2(CCC2)Oc2ccc(Br)cc21) `ZINC001462850841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462850841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001462850841 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC2(CCC2)Oc2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 16, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/723 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/723' -> `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]1CC2(CCC2)Oc2ccc(Br)cc21) `ZINC001462850841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462850841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001462850841 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC2(CCC2)Oc2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 45 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462850841 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841 Building ZINC001462850841 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462850841 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 722) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC2(CCC2)Oc2ccc(Br)cc21) `ZINC001462850841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462850841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001462850841 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC2(CCC2)Oc2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 16, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 104 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 723) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC2(CCC2)Oc2ccc(Br)cc21) `ZINC001462850841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462850841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001462850841 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC2(CCC2)Oc2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 45 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462850841 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850841 Building ZINC001462850844 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462850844 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/724 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/724' -> `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]1CC2(CCC2)Oc2ccc(Br)cc21) `ZINC001462850844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462850844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001462850844 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC2(CCC2)Oc2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 17, 30, 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, 30, 30, 30] 41 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/725 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/725' -> `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]1CC2(CCC2)Oc2ccc(Br)cc21) `ZINC001462850844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462850844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001462850844 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CC2(CCC2)Oc2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 16, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34] 43 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462850844 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844 Building ZINC001462850844 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462850844 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 724) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC2(CCC2)Oc2ccc(Br)cc21) `ZINC001462850844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462850844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001462850844 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CC2(CCC2)Oc2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 17, 30, 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, 30, 30, 30] 41 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 725) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CC2(CCC2)Oc2ccc(Br)cc21) `ZINC001462850844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462850844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001462850844 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CC2(CCC2)Oc2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 16, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34] 43 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462850844 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462850844 Building ZINC001462861958 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462861958 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/726 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(C)ccc2c1N(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c3ccccc3)c1C)CCC2) `ZINC001462861958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462861958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001462861958 none COC(=O)c1c(C)ccc2c1N(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c3ccccc3)c1C)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 5, 6, 6, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 6, 6, 4, 6, 6, 4, 4, 4, 2, 2, 2, 2, 2, 2] 8 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, 56]) total number of confs: 17 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/727 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(C)ccc2c1N(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c3ccccc3)c1C)CCC2) `ZINC001462861958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462861958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001462861958 none COC(=O)c1c(C)ccc2c1N(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c3ccccc3)c1C)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 6, 6, 6, 6, 6, 4, 4, 4, 2, 2, 2, 2, 2, 2] 8 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, 56]) total number of confs: 23 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462861958 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958 Building ZINC001462861958 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462861958 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 726) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)c1c(C)ccc2c1N(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c3ccccc3)c1C)CCC2) `ZINC001462861958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462861958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001462861958 none COC(=O)c1c(C)ccc2c1N(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c3ccccc3)c1C)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 5, 6, 6, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 6, 6, 4, 6, 6, 4, 4, 4, 2, 2, 2, 2, 2, 2] 8 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, 56]) total number of confs: 17 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 727) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)c1c(C)ccc2c1N(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c3ccccc3)c1C)CCC2) `ZINC001462861958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462861958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001462861958 none COC(=O)c1c(C)ccc2c1N(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c3ccccc3)c1C)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 6, 6, 6, 6, 6, 4, 4, 4, 2, 2, 2, 2, 2, 2] 8 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, 56]) total number of confs: 23 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462861958 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462861958 Building ZINC001462907110 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462907110 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/728 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1oc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1C(F)(F)F) `ZINC001462907110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462907110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001462907110 none CCOC(=O)c1oc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'C.2', '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', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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] 0 hydrogens 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, 31, 26, 6, 26, 6, 6, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 4, 4, 1, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/729 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1oc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1C(F)(F)F) `ZINC001462907110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462907110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001462907110 none CCOC(=O)c1oc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'C.2', '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', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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] 0 hydrogens 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, 31, 26, 6, 26, 6, 6, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 4, 4, 1, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462907110 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110 Building ZINC001462907110 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462907110 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 728) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1oc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1C(F)(F)F) `ZINC001462907110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462907110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001462907110 none CCOC(=O)c1oc(NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'C.2', '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', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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] 0 hydrogens 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, 31, 26, 6, 26, 6, 6, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 4, 4, 1, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 729) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1oc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1C(F)(F)F) `ZINC001462907110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462907110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001462907110 none CCOC(=O)c1oc(NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'O.3', 'C.2', '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', 'C.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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] 0 hydrogens 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, 31, 26, 6, 26, 6, 6, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 6, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 4, 4, 1, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462907110 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462907110 Building ZINC001462930764 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462930764 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/730 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1Cc2cc(F)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC001462930764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462930764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001462930764 none CC(C)(C)OC(=O)NC[C@@H]1Cc2cc(F)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 36, 46, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 17, 17, 5, 5, 5, 5, 5, 2, 2, 2, 2, 5, 5] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/731 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1Cc2cc(F)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC001462930764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462930764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001462930764 none CC(C)(C)OC(=O)NC[C@@H]1Cc2cc(F)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 38, 45, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 3, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 18, 18, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [49, 50, 51, 52, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 53, 54]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462930764 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764 Building ZINC001462930764 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462930764 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 730) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NC[C@@H]1Cc2cc(F)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC001462930764.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462930764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001462930764 none CC(C)(C)OC(=O)NC[C@@H]1Cc2cc(F)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 36, 46, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 17, 17, 5, 5, 5, 5, 5, 2, 2, 2, 2, 5, 5] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 731) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NC[C@@H]1Cc2cc(F)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC001462930764.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462930764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001462930764 none CC(C)(C)OC(=O)NC[C@@H]1Cc2cc(F)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 38, 45, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 3, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 18, 18, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [49, 50, 51, 52, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 53, 54]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462930764 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930764 Building ZINC001462930765 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462930765 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/732 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1Cc2cc(F)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC001462930765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462930765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001462930765 none CC(C)(C)OC(=O)NC[C@H]1Cc2cc(F)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 37, 43, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 3, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 17, 17, 5, 5, 5, 5, 5, 2, 2, 2, 2, 5, 5] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/733 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1Cc2cc(F)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC001462930765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462930765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001462930765 none CC(C)(C)OC(=O)NC[C@H]1Cc2cc(F)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 36, 45, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 15, 15, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 50, 51, 52, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 53, 54]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462930765 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765 Building ZINC001462930765 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462930765 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 732) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1Cc2cc(F)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC001462930765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462930765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001462930765 none CC(C)(C)OC(=O)NC[C@H]1Cc2cc(F)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 37, 43, 17, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 3, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 17, 17, 5, 5, 5, 5, 5, 2, 2, 2, 2, 5, 5] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 733) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1Cc2cc(F)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1) `ZINC001462930765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462930765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001462930765 none CC(C)(C)OC(=O)NC[C@H]1Cc2cc(F)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 36, 45, 15, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 15, 15, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [49, 50, 51, 52, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 53, 54]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462930765 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462930765 Building ZINC001462978237 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462978237 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/734 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H](C[C@@H]2COCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001462978237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462978237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001462978237 none CC(C)(C)OC(=O)N1C[C@H](C[C@@H]2COCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 26, 36, 26, 26, 19, 26, 13, 13, 13, 13, 13, 13, 13, 12, 2, 12, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 19, 19, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 50 rigid atoms, others: [54, 57, 55, 56, 52, 21, 22, 23, 24, 25, 26, 59, 60, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/735 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H](C[C@@H]2COCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001462978237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462978237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001462978237 none CC(C)(C)OC(=O)N1C[C@H](C[C@@H]2COCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 19, 35, 19, 19, 13, 19, 7, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 13, 13, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19] 50 rigid atoms, others: [54, 57, 55, 56, 19, 52, 21, 22, 23, 24, 25, 26, 59, 60, 58, 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, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 143 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462978237 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237 Building ZINC001462978237 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462978237 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 734) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H](C[C@@H]2COCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001462978237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462978237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001462978237 none CC(C)(C)OC(=O)N1C[C@H](C[C@@H]2COCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 26, 36, 26, 26, 19, 26, 13, 13, 13, 13, 13, 13, 13, 12, 2, 12, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 19, 19, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 50 rigid atoms, others: [54, 57, 55, 56, 52, 21, 22, 23, 24, 25, 26, 59, 60, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 148 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 735) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/735: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H](C[C@@H]2COCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001462978237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462978237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001462978237 none CC(C)(C)OC(=O)N1C[C@H](C[C@@H]2COCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 19, 35, 19, 19, 13, 19, 7, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 13, 13, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19] 50 rigid atoms, others: [54, 57, 55, 56, 19, 52, 21, 22, 23, 24, 25, 26, 59, 60, 58, 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, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 143 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462978237 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978237 Building ZINC001462978250 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462978250 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/736 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](C[C@@H]2COCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001462978250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462978250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001462978250 none CC(C)(C)OC(=O)N1C[C@@H](C[C@@H]2COCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 30, 36, 30, 30, 26, 30, 15, 15, 15, 15, 15, 15, 15, 13, 2, 13, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 26, 26, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30] 50 rigid atoms, others: [54, 57, 55, 56, 52, 21, 22, 23, 24, 25, 26, 59, 60, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 155 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/737 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](C[C@@H]2COCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001462978250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462978250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001462978250 none CC(C)(C)OC(=O)N1C[C@@H](C[C@@H]2COCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 21, 38, 21, 21, 18, 21, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 18, 18, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21] 50 rigid atoms, others: [54, 57, 55, 56, 52, 21, 22, 23, 24, 25, 26, 59, 60, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 152 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462978250 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250 Building ZINC001462978250 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462978250 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 736) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/736: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](C[C@@H]2COCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001462978250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462978250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001462978250 none CC(C)(C)OC(=O)N1C[C@@H](C[C@@H]2COCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 30, 36, 30, 30, 26, 30, 15, 15, 15, 15, 15, 15, 15, 13, 2, 13, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 26, 26, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30] 50 rigid atoms, others: [54, 57, 55, 56, 52, 21, 22, 23, 24, 25, 26, 59, 60, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 155 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 737) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/737: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](C[C@@H]2COCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001462978250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462978250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001462978250 none CC(C)(C)OC(=O)N1C[C@@H](C[C@@H]2COCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 21, 38, 21, 21, 18, 21, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 18, 18, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21] 50 rigid atoms, others: [54, 57, 55, 56, 52, 21, 22, 23, 24, 25, 26, 59, 60, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 152 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462978250 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978250 Building ZINC001462978264 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462978264 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/738 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H](C[C@H]2COCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001462978264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462978264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001462978264 none CC(C)(C)OC(=O)N1C[C@H](C[C@H]2COCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 21, 36, 21, 21, 18, 21, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 18, 18, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21] 50 rigid atoms, others: [54, 57, 55, 56, 52, 21, 22, 23, 24, 25, 26, 59, 60, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 142 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/739 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H](C[C@H]2COCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001462978264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462978264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001462978264 none CC(C)(C)OC(=O)N1C[C@H](C[C@H]2COCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 27, 35, 27, 27, 24, 27, 14, 14, 14, 14, 14, 14, 14, 13, 2, 13, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 24, 24, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [54, 57, 55, 56, 52, 21, 22, 23, 24, 25, 26, 59, 60, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 147 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462978264 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264 Building ZINC001462978264 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462978264 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 738) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H](C[C@H]2COCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001462978264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462978264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001462978264 none CC(C)(C)OC(=O)N1C[C@H](C[C@H]2COCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 36, 21, 36, 21, 21, 18, 21, 9, 9, 9, 9, 9, 9, 9, 8, 2, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 18, 18, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21] 50 rigid atoms, others: [54, 57, 55, 56, 52, 21, 22, 23, 24, 25, 26, 59, 60, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 142 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 739) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@H](C[C@H]2COCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001462978264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462978264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001462978264 none CC(C)(C)OC(=O)N1C[C@H](C[C@H]2COCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 27, 35, 27, 27, 24, 27, 14, 14, 14, 14, 14, 14, 14, 13, 2, 13, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 24, 24, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27] 50 rigid atoms, others: [54, 57, 55, 56, 52, 21, 22, 23, 24, 25, 26, 59, 60, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 147 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462978264 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978264 Building ZINC001462978280 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462978280 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/740 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](C[C@H]2COCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001462978280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462978280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001462978280 none CC(C)(C)OC(=O)N1C[C@@H](C[C@H]2COCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 18, 33, 18, 18, 12, 18, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 12, 12, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 50 rigid atoms, others: [54, 57, 55, 56, 52, 21, 22, 23, 24, 25, 26, 59, 60, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 135 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/741 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](C[C@H]2COCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001462978280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462978280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001462978280 none CC(C)(C)OC(=O)N1C[C@@H](C[C@H]2COCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 25, 37, 25, 25, 19, 25, 13, 13, 13, 13, 13, 13, 13, 12, 2, 12, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 19, 19, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [54, 57, 55, 56, 52, 21, 22, 23, 24, 25, 26, 59, 60, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462978280 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280 Building ZINC001462978280 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462978280 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 740) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1C[C@@H](C[C@H]2COCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001462978280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462978280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001462978280 none CC(C)(C)OC(=O)N1C[C@@H](C[C@H]2COCCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 18, 33, 18, 18, 12, 18, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 12, 12, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 50 rigid atoms, others: [54, 57, 55, 56, 52, 21, 22, 23, 24, 25, 26, 59, 60, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 135 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 741) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1C[C@@H](C[C@H]2COCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21) `ZINC001462978280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462978280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001462978280 none CC(C)(C)OC(=O)N1C[C@@H](C[C@H]2COCCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 25, 37, 25, 25, 19, 25, 13, 13, 13, 13, 13, 13, 13, 12, 2, 12, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 19, 19, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 rigid atoms, others: [54, 57, 55, 56, 52, 21, 22, 23, 24, 25, 26, 59, 60, 58, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462978280 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462978280 Building ZINC001462995245 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462995245 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/742 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2c(c3ccc(F)cc3)nc3ccc(F)cn32)cn1) `ZINC001462995245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462995245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001462995245 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2c(c3ccc(F)cc3)nc3ccc(F)cn32)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.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'C.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, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 7, 7, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 25, 25, 32, 32, 31, 32, 32, 32, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 13, 13, 32, 32, 32, 32, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/743 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2c(c3ccc(F)cc3)nc3ccc(F)cn32)cn1) `ZINC001462995245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462995245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001462995245 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2c(c3ccc(F)cc3)nc3ccc(F)cn32)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.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'C.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, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 7, 7, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 33, 33, 33, 33, 33, 33, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 12, 12, 33, 33, 33, 33, 24, 24, 24, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462995245 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245 Building ZINC001462995245 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001462995245 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 742) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2c(c3ccc(F)cc3)nc3ccc(F)cn32)cn1) `ZINC001462995245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001462995245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001462995245 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2c(c3ccc(F)cc3)nc3ccc(F)cn32)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.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'C.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, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 7, 7, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 25, 25, 32, 32, 31, 32, 32, 32, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 13, 13, 32, 32, 32, 32, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 743) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2c(c3ccc(F)cc3)nc3ccc(F)cn32)cn1) `ZINC001462995245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001462995245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001462995245 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2c(c3ccc(F)cc3)nc3ccc(F)cn32)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.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'C.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, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 15, 1, 8, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 7, 7, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 24, 24, 33, 33, 33, 33, 33, 33, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 12, 12, 33, 33, 33, 33, 24, 24, 24, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001462995245 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001462995245 Building ZINC001463001397 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463001397 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/744 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cc(C2CC2)nn1C) `ZINC001463001397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463001397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001463001397 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cc(C2CC2)nn1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 14, 14, 14, 15, 15, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 14, 15, 15, 15, 15, 15, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/745 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cc(C2CC2)nn1C) `ZINC001463001397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463001397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001463001397 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cc(C2CC2)nn1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463001397 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397 Building ZINC001463001397 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463001397 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 744) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cc(C2CC2)nn1C) `ZINC001463001397.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463001397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001463001397 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cc(C2CC2)nn1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 14, 14, 14, 15, 15, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 14, 15, 15, 15, 15, 15, 14, 14, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 745) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cc(C2CC2)nn1C) `ZINC001463001397.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463001397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001463001397 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cc(C2CC2)nn1C 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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 5, 5, 8, 8, 5, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463001397 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463001397 Building ZINC001463047871 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463047871 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/746 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCn2nc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2C1) `ZINC001463047871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463047871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001463047871 none CC(C)(C)OC(=O)N1CCn2nc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', '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', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 27, 16, 27, 16, 16, 16, 16, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 16, 44, 44, 44, 44, 44, 44, 44, 44, 44, 16, 16, 16, 16, 4, 3, 1, 3, 8, 16, 16] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/747 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCn2nc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2C1) `ZINC001463047871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463047871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001463047871 none CC(C)(C)OC(=O)N1CCn2nc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', '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', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 26, 15, 26, 15, 15, 15, 15, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 15, 42, 42, 42, 42, 42, 42, 42, 42, 42, 15, 15, 15, 15, 4, 3, 1, 3, 8, 15, 15] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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/6899/xaj-8058088.10/working/building/ZINC001463047871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463047871 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871 Building ZINC001463047871 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463047871 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 746) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCn2nc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2C1) `ZINC001463047871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463047871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001463047871 none CC(C)(C)OC(=O)N1CCn2nc(NC(=O)[C@@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', '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', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 27, 16, 27, 16, 16, 16, 16, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 16, 44, 44, 44, 44, 44, 44, 44, 44, 44, 16, 16, 16, 16, 4, 3, 1, 3, 8, 16, 16] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 747) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCn2nc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2C1) `ZINC001463047871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463047871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001463047871 none CC(C)(C)OC(=O)N1CCn2nc(NC(=O)[C@]([O-])([SiH3])c3cc(Cl)cc(Cl)c3)cc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', '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', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 1, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 26, 15, 26, 15, 15, 15, 15, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 15, 42, 42, 42, 42, 42, 42, 42, 42, 42, 15, 15, 15, 15, 4, 3, 1, 3, 8, 15, 15] 50 rigid atoms, others: [14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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/6899/xaj-8058088.10/working/building/ZINC001463047871 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463047871 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463047871 Building ZINC001463063546 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463063546 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/748 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1(CNC(=O)OC(C)(C)C)CCOCC1) `ZINC001463063546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463063546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001463063546 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1(CNC(=O)OC(C)(C)C)CCOCC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 3, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 13, 18, 28, 39, 39, 50, 50, 50, 50, 13, 13, 13, 13, 13, 5, 5, 5, 2, 1, 2, 18, 18, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 163 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/749 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1(CNC(=O)OC(C)(C)C)CCOCC1) `ZINC001463063546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463063546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001463063546 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1(CNC(=O)OC(C)(C)C)CCOCC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 1, 2, 2, 2, 4, 12, 18, 27, 38, 38, 50, 50, 50, 50, 12, 12, 12, 12, 12, 4, 4, 4, 2, 1, 2, 18, 18, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 165 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463063546 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546 Building ZINC001463063546 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463063546 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 748) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1(CNC(=O)OC(C)(C)C)CCOCC1) `ZINC001463063546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463063546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001463063546 none CN(C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1(CNC(=O)OC(C)(C)C)CCOCC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 3, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 5, 13, 18, 28, 39, 39, 50, 50, 50, 50, 13, 13, 13, 13, 13, 5, 5, 5, 2, 1, 2, 18, 18, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 163 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 749) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1(CNC(=O)OC(C)(C)C)CCOCC1) `ZINC001463063546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463063546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001463063546 none CN(C(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1)C1(CNC(=O)OC(C)(C)C)CCOCC1 NO_LONG_NAME dock atom types: ['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', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 1, 2, 2, 2, 4, 12, 18, 27, 38, 38, 50, 50, 50, 50, 12, 12, 12, 12, 12, 4, 4, 4, 2, 1, 2, 18, 18, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 165 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463063546 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463063546 Building ZINC001463064543 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463064543 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/750 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2NC(=O)OC(C)(C)C)cc1Cl) `ZINC001463064543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463064543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001463064543 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2NC(=O)OC(C)(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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] 0 hydrogens 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, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 24, 24, 25, 25, 25, 25, 4, 4, 4, 8, 8, 8, 4, 4, 2, 11, 11, 11, 11, 11, 11, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 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, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/751 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/751' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2NC(=O)OC(C)(C)C)cc1Cl) `ZINC001463064543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463064543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001463064543 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2NC(=O)OC(C)(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 26, 26, 29, 29, 29, 29, 5, 5, 5, 9, 9, 9, 5, 5, 2, 11, 11, 11, 11, 11, 11, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463064543 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543 Building ZINC001463064543 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463064543 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 750) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2NC(=O)OC(C)(C)C)cc1Cl) `ZINC001463064543.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463064543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001463064543 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2NC(=O)OC(C)(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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] 0 hydrogens 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, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 24, 24, 25, 25, 25, 25, 4, 4, 4, 8, 8, 8, 4, 4, 2, 11, 11, 11, 11, 11, 11, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25, 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, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 751) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2NC(=O)OC(C)(C)C)cc1Cl) `ZINC001463064543.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463064543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001463064543 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2NC(=O)OC(C)(C)C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 19, 26, 26, 29, 29, 29, 29, 5, 5, 5, 9, 9, 9, 5, 5, 2, 11, 11, 11, 11, 11, 11, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463064543 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463064543 Building ZINC001463191471 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463191471 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/752 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1Br) `ZINC001463191471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463191471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001463191471 none COCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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: [29, 29, 29, 15, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 5, 3, 3, 3, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 7, 7, 2, 3, 3, 5, 5, 5, 3, 7] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/753 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1Br) `ZINC001463191471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463191471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001463191471 none COCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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: [30, 30, 30, 16, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 5, 3, 3, 3, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 7, 7, 2, 3, 3, 5, 5, 5, 3, 7] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463191471 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471 Building ZINC001463191471 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463191471 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 752) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1Br) `ZINC001463191471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463191471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001463191471 none COCCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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: [29, 29, 29, 15, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 5, 3, 3, 3, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 7, 7, 2, 3, 3, 5, 5, 5, 3, 7] 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 753) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1Br) `ZINC001463191471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463191471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001463191471 none COCCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 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: [30, 30, 30, 16, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 5, 3, 3, 3, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 7, 7, 2, 3, 3, 5, 5, 5, 3, 7] 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463191471 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463191471 Building ZINC001463214856 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463214856 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/754 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/754' -> `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)c1ccc(C(F)(F)F)cc1) `ZINC001463214856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463214856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001463214856 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C(F)(F)F)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 13, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 11, 6, 6, 6, 5, 10, 10, 8, 9, 10, 10, 10, 10, 10, 13, 13, 13, 3, 6, 6, 11, 11, 11, 6, 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/755 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/755' -> `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)c1ccc(C(F)(F)F)cc1) `ZINC001463214856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463214856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001463214856 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C(F)(F)F)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 14, 3, 6, 3, 1, 3, 1, 1, 1, 5, 5, 2, 5, 10, 5, 5, 5, 6, 12, 12, 9, 11, 12, 12, 12, 12, 12, 14, 14, 14, 3, 5, 5, 10, 10, 10, 5, 12, 12, 12, 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: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463214856 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856 Building ZINC001463214856 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463214856 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 754) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C(F)(F)F)cc1) `ZINC001463214856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463214856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001463214856 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C(F)(F)F)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 13, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 11, 6, 6, 6, 5, 10, 10, 8, 9, 10, 10, 10, 10, 10, 13, 13, 13, 3, 6, 6, 11, 11, 11, 6, 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 755) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C(F)(F)F)cc1) `ZINC001463214856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463214856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001463214856 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C(F)(F)F)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 14, 3, 6, 3, 1, 3, 1, 1, 1, 5, 5, 2, 5, 10, 5, 5, 5, 6, 12, 12, 9, 11, 12, 12, 12, 12, 12, 14, 14, 14, 3, 5, 5, 10, 10, 10, 5, 12, 12, 12, 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: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463214856 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214856 Building ZINC001463214864 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463214864 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/756 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/756' -> `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)c1ccc(C(F)(F)F)cc1) `ZINC001463214864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463214864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001463214864 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C(F)(F)F)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 14, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 6, 13, 13, 6, 6, 13, 13, 13, 13, 13, 14, 14, 14, 3, 4, 4, 9, 9, 9, 4, 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, 38, 39, 40, 41, 42, 43]) total number of confs: 125 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/757 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/757' -> `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)c1ccc(C(F)(F)F)cc1) `ZINC001463214864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463214864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001463214864 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C(F)(F)F)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 13, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 10, 6, 6, 6, 5, 11, 11, 5, 5, 11, 11, 11, 11, 11, 13, 13, 13, 3, 6, 6, 10, 10, 10, 6, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463214864 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864 Building ZINC001463214864 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463214864 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 756) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C(F)(F)F)cc1) `ZINC001463214864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463214864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001463214864 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C(F)(F)F)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 14, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 6, 13, 13, 6, 6, 13, 13, 13, 13, 13, 14, 14, 14, 3, 4, 4, 9, 9, 9, 4, 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, 38, 39, 40, 41, 42, 43]) total number of confs: 125 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 757) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C(F)(F)F)cc1) `ZINC001463214864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463214864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001463214864 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccc(C(F)(F)F)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 13, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 10, 6, 6, 6, 5, 11, 11, 5, 5, 11, 11, 11, 11, 11, 13, 13, 13, 3, 6, 6, 10, 10, 10, 6, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463214864 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463214864 Building ZINC001463237552 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463237552 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/758 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(C)c3cc(C(F)(F)F)ccc32)cc1Cl) `ZINC001463237552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463237552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001463237552 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(C)c3cc(C(F)(F)F)ccc32)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.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 8, 8, 1, 1, 1, 2, 8, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 15, 15, 15, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 73 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/759 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(C)c3cc(C(F)(F)F)ccc32)cc1Cl) `ZINC001463237552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463237552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001463237552 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(C)c3cc(C(F)(F)F)ccc32)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.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 8, 8, 1, 1, 1, 2, 8, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 15, 15, 15, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 73 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463237552 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552 Building ZINC001463237552 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463237552 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 758) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(C)c3cc(C(F)(F)F)ccc32)cc1Cl) `ZINC001463237552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463237552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001463237552 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC(=O)N(C)c3cc(C(F)(F)F)ccc32)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.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 8, 8, 1, 1, 1, 2, 8, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 15, 15, 15, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 73 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 759) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(C)c3cc(C(F)(F)F)ccc32)cc1Cl) `ZINC001463237552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463237552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001463237552 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC(=O)N(C)c3cc(C(F)(F)F)ccc32)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.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 8, 8, 1, 1, 1, 2, 8, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 8, 8, 15, 15, 15, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 73 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463237552 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463237552 Building ZINC001463329029 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463329029 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/760 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc2nc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)[nH]c2c(Br)c1) `ZINC001463329029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463329029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001463329029 none COC(=O)c1cc2nc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)[nH]c2c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 47, 13, 13, 13, 13, 12, 12, 1, 12, 1, 1, 1, 6, 6, 1, 1, 6, 6, 13, 13, 13, 13, 13, 13, 47, 47, 47, 13, 12, 6, 6, 6, 6, 13] 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/761 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc2nc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)[nH]c2c(Br)c1) `ZINC001463329029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463329029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001463329029 none COC(=O)c1cc2nc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)[nH]c2c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 47, 13, 13, 13, 13, 12, 12, 1, 12, 1, 1, 1, 6, 6, 1, 6, 6, 6, 13, 13, 13, 13, 13, 13, 47, 47, 47, 13, 12, 6, 6, 6, 6, 13] 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: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463329029 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029 Building ZINC001463329029 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463329029 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 760) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)c1cc2nc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)[nH]c2c(Br)c1) `ZINC001463329029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463329029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001463329029 none COC(=O)c1cc2nc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)[nH]c2c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 47, 13, 13, 13, 13, 12, 12, 1, 12, 1, 1, 1, 6, 6, 1, 1, 6, 6, 13, 13, 13, 13, 13, 13, 47, 47, 47, 13, 12, 6, 6, 6, 6, 13] 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: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 761) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)c1cc2nc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)[nH]c2c(Br)c1) `ZINC001463329029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463329029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001463329029 none COC(=O)c1cc2nc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)[nH]c2c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 6, 1, 1, 17, 1, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 47, 13, 13, 13, 13, 12, 12, 1, 12, 1, 1, 1, 6, 6, 1, 6, 6, 6, 13, 13, 13, 13, 13, 13, 47, 47, 47, 13, 12, 6, 6, 6, 6, 13] 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: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463329029 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463329029 Building ZINC001463434538 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463434538 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/762 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001463434538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463434538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001463434538 none CC(C)(C)OC(=O)N1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 38, 31, 38, 31, 31, 31, 31, 15, 31, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 45, 45, 45, 45, 45, 45, 45, 45, 45, 31, 31, 31, 31, 31, 31, 11, 11, 3, 6, 6, 31, 31, 31, 31] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/763 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001463434538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463434538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001463434538 none CC(C)(C)OC(=O)N1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 41, 36, 41, 36, 36, 36, 36, 14, 36, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 36, 36, 45, 45, 45, 45, 45, 45, 45, 45, 45, 36, 36, 36, 36, 36, 36, 12, 12, 3, 5, 5, 36, 36, 36, 36] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463434538 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538 Building ZINC001463434538 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463434538 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 762) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001463434538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463434538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001463434538 none CC(C)(C)OC(=O)N1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 38, 31, 38, 31, 31, 31, 31, 15, 31, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 45, 45, 45, 45, 45, 45, 45, 45, 45, 31, 31, 31, 31, 31, 31, 11, 11, 3, 6, 6, 31, 31, 31, 31] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 763) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001463434538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463434538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001463434538 none CC(C)(C)OC(=O)N1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 41, 36, 41, 36, 36, 36, 36, 14, 36, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 36, 36, 45, 45, 45, 45, 45, 45, 45, 45, 45, 36, 36, 36, 36, 36, 36, 12, 12, 3, 5, 5, 36, 36, 36, 36] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463434538 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434538 Building ZINC001463434545 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463434545 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/764 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001463434545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463434545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001463434545 none CC(C)(C)OC(=O)N1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 35, 44, 35, 35, 35, 35, 19, 35, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 35, 35, 44, 44, 44, 44, 44, 44, 44, 44, 44, 35, 35, 35, 35, 35, 35, 11, 11, 2, 7, 7, 35, 35, 35, 35] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/765 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001463434545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463434545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001463434545 none CC(C)(C)OC(=O)N1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 45, 35, 45, 35, 35, 35, 35, 22, 35, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 35, 35, 48, 48, 48, 48, 48, 48, 48, 48, 48, 35, 35, 35, 35, 35, 35, 13, 13, 2, 5, 5, 35, 35, 35, 35] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463434545 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545 Building ZINC001463434545 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463434545 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 764) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001463434545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463434545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001463434545 none CC(C)(C)OC(=O)N1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 35, 44, 35, 35, 35, 35, 19, 35, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 35, 35, 44, 44, 44, 44, 44, 44, 44, 44, 44, 35, 35, 35, 35, 35, 35, 11, 11, 2, 7, 7, 35, 35, 35, 35] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 765) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001463434545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463434545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001463434545 none CC(C)(C)OC(=O)N1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 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] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 45, 35, 45, 35, 35, 35, 35, 22, 35, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 35, 35, 48, 48, 48, 48, 48, 48, 48, 48, 48, 35, 35, 35, 35, 35, 35, 13, 13, 2, 5, 5, 35, 35, 35, 35] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463434545 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463434545 Building ZINC001463451378 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463451378 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/766 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(CC(F)(F)F)C2CCN(C(=O)OC(C)(C)C)CC2)cc1) `ZINC001463451378.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463451378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001463451378 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N(CC(F)(F)F)C2CCN(C(=O)OC(C)(C)C)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', 'F', 'F', 'F', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 15, 15, 5, 5, 5, 8, 1, 11, 12, 5, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 8, 10, 10, 10, 10, 9, 12, 12, 12, 12, 27, 27, 47, 47, 47, 47, 12, 12, 3, 3, 3, 3, 3, 3, 3, 10, 10, 12, 12, 12, 12, 12, 47, 47, 47, 47, 47, 47, 47, 47, 47, 12, 12, 12, 12, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/767 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N(CC(F)(F)F)C2CCN(C(=O)OC(C)(C)C)CC2)cc1) `ZINC001463451378.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463451378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001463451378 none Cc1ccc([C@]([O-])([SiH3])C(=O)N(CC(F)(F)F)C2CCN(C(=O)OC(C)(C)C)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', 'F', 'F', 'F', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 15, 15, 5, 5, 5, 8, 1, 11, 12, 5, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 7, 10, 10, 10, 10, 9, 13, 13, 13, 13, 27, 27, 47, 47, 47, 47, 13, 11, 3, 3, 3, 3, 3, 3, 3, 10, 10, 13, 13, 13, 13, 13, 47, 47, 47, 47, 47, 47, 47, 47, 47, 13, 13, 13, 13, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 157 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463451378 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378 Building ZINC001463451378 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463451378 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 766) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N(CC(F)(F)F)C2CCN(C(=O)OC(C)(C)C)CC2)cc1) `ZINC001463451378.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463451378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001463451378 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N(CC(F)(F)F)C2CCN(C(=O)OC(C)(C)C)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', 'F', 'F', 'F', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 15, 15, 5, 5, 5, 8, 1, 11, 12, 5, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 8, 10, 10, 10, 10, 9, 12, 12, 12, 12, 27, 27, 47, 47, 47, 47, 12, 12, 3, 3, 3, 3, 3, 3, 3, 10, 10, 12, 12, 12, 12, 12, 47, 47, 47, 47, 47, 47, 47, 47, 47, 12, 12, 12, 12, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 767) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N(CC(F)(F)F)C2CCN(C(=O)OC(C)(C)C)CC2)cc1) `ZINC001463451378.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463451378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001463451378 none Cc1ccc([C@]([O-])([SiH3])C(=O)N(CC(F)(F)F)C2CCN(C(=O)OC(C)(C)C)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', 'F', 'F', 'F', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 15, 15, 15, 5, 5, 5, 8, 1, 11, 12, 5, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 7, 10, 10, 10, 10, 9, 13, 13, 13, 13, 27, 27, 47, 47, 47, 47, 13, 11, 3, 3, 3, 3, 3, 3, 3, 10, 10, 13, 13, 13, 13, 13, 47, 47, 47, 47, 47, 47, 47, 47, 47, 13, 13, 13, 13, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 157 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463451378 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451378 Building ZINC001463451549 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463451549 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/768 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)n2)C1) `ZINC001463451549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463451549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001463451549 none CC(C)(C)OC(=O)N1CC[C@H](c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 25, 42, 25, 25, 25, 6, 25, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 3, 3, 2, 2, 2, 2, 2, 25, 25] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/769 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](c2ccnc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)n2)C1) `ZINC001463451549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463451549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001463451549 none CC(C)(C)OC(=O)N1CC[C@H](c2ccnc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 28, 47, 28, 28, 28, 6, 28, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 3, 3, 2, 2, 2, 2, 2, 28, 28] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463451549 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549 Building ZINC001463451549 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463451549 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 768) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@H](c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)n2)C1) `ZINC001463451549.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463451549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001463451549 none CC(C)(C)OC(=O)N1CC[C@H](c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 25, 42, 25, 25, 25, 6, 25, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25, 3, 3, 2, 2, 2, 2, 2, 25, 25] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 769) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@H](c2ccnc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)n2)C1) `ZINC001463451549.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463451549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001463451549 none CC(C)(C)OC(=O)N1CC[C@H](c2ccnc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 28, 47, 28, 28, 28, 6, 28, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 3, 3, 2, 2, 2, 2, 2, 28, 28] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463451549 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451549 Building ZINC001463451552 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463451552 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/770 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)n2)C1) `ZINC001463451552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463451552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001463451552 none CC(C)(C)OC(=O)N1CC[C@@H](c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 28, 47, 28, 28, 28, 6, 28, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 3, 3, 2, 2, 2, 2, 2, 28, 28] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/771 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](c2ccnc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)n2)C1) `ZINC001463451552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463451552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001463451552 none CC(C)(C)OC(=O)N1CC[C@@H](c2ccnc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 26, 43, 26, 26, 26, 6, 26, 3, 2, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 2, 3, 2, 2, 2, 2, 2, 26, 26] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463451552 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552 Building ZINC001463451552 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463451552 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 770) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@@H](c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)n2)C1) `ZINC001463451552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463451552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001463451552 none CC(C)(C)OC(=O)N1CC[C@@H](c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 28, 47, 28, 28, 28, 6, 28, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 3, 3, 2, 2, 2, 2, 2, 28, 28] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 154 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 771) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@@H](c2ccnc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)n2)C1) `ZINC001463451552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463451552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001463451552 none CC(C)(C)OC(=O)N1CC[C@@H](c2ccnc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 26, 43, 26, 26, 26, 6, 26, 3, 2, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 2, 3, 2, 2, 2, 2, 2, 26, 26] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463451552 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463451552 Building ZINC001463452011 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463452011 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/772 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)n2)C1) `ZINC001463452011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463452011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463452011 none CC(C)(C)OC(=O)N1CC[C@@H](c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 41, 25, 41, 25, 25, 25, 6, 25, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 3, 25, 43, 43, 43, 43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 3, 3, 2, 4, 4, 25, 25] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/773 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](c2ccnc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)n2)C1) `ZINC001463452011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463452011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463452011 none CC(C)(C)OC(=O)N1CC[C@@H](c2ccnc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 39, 24, 39, 24, 24, 24, 5, 24, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 3, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 24, 24, 24, 24, 3, 3, 2, 4, 4, 24, 24] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463452011 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011 Building ZINC001463452011 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463452011 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 772) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)n2)C1) `ZINC001463452011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463452011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463452011 none CC(C)(C)OC(=O)N1CC[C@@H](c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 41, 25, 41, 25, 25, 25, 6, 25, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 3, 25, 43, 43, 43, 43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 3, 3, 2, 4, 4, 25, 25] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 773) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](c2ccnc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)n2)C1) `ZINC001463452011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463452011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463452011 none CC(C)(C)OC(=O)N1CC[C@@H](c2ccnc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 39, 24, 39, 24, 24, 24, 5, 24, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 3, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 24, 24, 24, 24, 3, 3, 2, 4, 4, 24, 24] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463452011 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452011 Building ZINC001463452017 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463452017 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/774 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)n2)C1) `ZINC001463452017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463452017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463452017 none CC(C)(C)OC(=O)N1CC[C@H](c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 38, 23, 38, 23, 23, 23, 5, 23, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 3, 23, 40, 40, 40, 40, 40, 40, 40, 40, 40, 23, 23, 23, 23, 3, 3, 2, 4, 4, 23, 23] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/775 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](c2ccnc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)n2)C1) `ZINC001463452017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463452017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463452017 none CC(C)(C)OC(=O)N1CC[C@H](c2ccnc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 41, 25, 41, 25, 25, 25, 6, 25, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 3, 25, 43, 43, 43, 43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 3, 3, 2, 4, 4, 25, 25] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463452017 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017 Building ZINC001463452017 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463452017 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 774) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/774: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)n2)C1) `ZINC001463452017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463452017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463452017 none CC(C)(C)OC(=O)N1CC[C@H](c2ccnc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)s3)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 38, 23, 38, 23, 23, 23, 5, 23, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 3, 23, 40, 40, 40, 40, 40, 40, 40, 40, 40, 23, 23, 23, 23, 3, 3, 2, 4, 4, 23, 23] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 775) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/775: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](c2ccnc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)n2)C1) `ZINC001463452017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463452017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463452017 none CC(C)(C)OC(=O)N1CC[C@H](c2ccnc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)s3)n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 8, 5, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 41, 25, 41, 25, 25, 25, 6, 25, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 3, 25, 43, 43, 43, 43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 3, 3, 2, 4, 4, 25, 25] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463452017 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452017 Building ZINC001463452083 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463452083 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/776 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(CC(F)(F)F)C2CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC001463452083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463452083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001463452083 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(CC(F)(F)F)C2CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 12, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 5, 7, 7, 7, 7, 6, 6, 6, 6, 6, 14, 14, 24, 25, 25, 25, 6, 6, 6, 6, 6, 6, 2, 6, 6, 7, 7, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 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]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/777 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N(CC(F)(F)F)C2CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC001463452083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463452083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001463452083 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(CC(F)(F)F)C2CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 12, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 5, 7, 7, 7, 7, 6, 6, 6, 6, 6, 14, 14, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 2, 6, 6, 7, 7, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 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]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463452083 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083 Building ZINC001463452083 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463452083 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 776) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)N(CC(F)(F)F)C2CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC001463452083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463452083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001463452083 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N(CC(F)(F)F)C2CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 12, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 5, 7, 7, 7, 7, 6, 6, 6, 6, 6, 14, 14, 24, 25, 25, 25, 6, 6, 6, 6, 6, 6, 2, 6, 6, 7, 7, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 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]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 777) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@]([O-])([SiH3])C(=O)N(CC(F)(F)F)C2CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC001463452083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463452083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001463452083 none Cc1cccc([C@]([O-])([SiH3])C(=O)N(CC(F)(F)F)C2CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 5, 8, 1, 11, 12, 5, 5, 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, 9, 8, 10, 11, 6, 7, 7, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 5, 7, 7, 7, 7, 6, 6, 6, 6, 6, 14, 14, 25, 25, 25, 25, 6, 6, 6, 6, 6, 6, 2, 6, 6, 7, 7, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 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]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463452083 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463452083 Building ZINC001463530253 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001463530253 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/778 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463530253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530253 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 13, 21, 21, 13, 21, 21, 4, 6, 6, 6, 12, 12, 12, 6, 6, 3, 4, 4, 4, 4, 13, 13, 21, 21, 13, 21, 21, 4, 4, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/779 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463530253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530253 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 15, 23, 23, 15, 23, 23, 5, 6, 6, 6, 15, 15, 15, 6, 6, 4, 5, 5, 5, 5, 15, 15, 23, 23, 15, 23, 23, 5, 5, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/780 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/780' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530253.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001463530253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530253 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 13, 21, 21, 13, 21, 21, 4, 6, 6, 6, 12, 12, 12, 6, 6, 3, 4, 4, 4, 4, 13, 13, 21, 21, 13, 21, 21, 4, 4, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/781 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/781' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530253.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001463530253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530253 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 15, 23, 23, 15, 23, 23, 5, 6, 6, 6, 15, 15, 15, 6, 6, 4, 5, 5, 5, 5, 15, 15, 23, 23, 15, 23, 23, 5, 5, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463530253 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 Building ZINC001463530253 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001463530253 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 778) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463530253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530253 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 13, 21, 21, 13, 21, 21, 4, 6, 6, 6, 12, 12, 12, 6, 6, 3, 4, 4, 4, 4, 13, 13, 21, 21, 13, 21, 21, 4, 4, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 779) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463530253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530253 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 15, 23, 23, 15, 23, 23, 5, 6, 6, 6, 15, 15, 15, 6, 6, 4, 5, 5, 5, 5, 15, 15, 23, 23, 15, 23, 23, 5, 5, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 780) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530253.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001463530253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530253 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 13, 21, 21, 13, 21, 21, 4, 6, 6, 6, 12, 12, 12, 6, 6, 3, 4, 4, 4, 4, 13, 13, 21, 21, 13, 21, 21, 4, 4, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 781) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530253.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001463530253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530253 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 15, 23, 23, 15, 23, 23, 5, 6, 6, 6, 15, 15, 15, 6, 6, 4, 5, 5, 5, 5, 15, 15, 23, 23, 15, 23, 23, 5, 5, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463530253 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 Building ZINC001463530253 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001463530253 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 778) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463530253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530253 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 13, 21, 21, 13, 21, 21, 4, 6, 6, 6, 12, 12, 12, 6, 6, 3, 4, 4, 4, 4, 13, 13, 21, 21, 13, 21, 21, 4, 4, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 779) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463530253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530253 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 15, 23, 23, 15, 23, 23, 5, 6, 6, 6, 15, 15, 15, 6, 6, 4, 5, 5, 5, 5, 15, 15, 23, 23, 15, 23, 23, 5, 5, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 780) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530253.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001463530253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530253 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 13, 21, 21, 13, 21, 21, 4, 6, 6, 6, 12, 12, 12, 6, 6, 3, 4, 4, 4, 4, 13, 13, 21, 21, 13, 21, 21, 4, 4, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 781) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530253.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001463530253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530253 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 15, 23, 23, 15, 23, 23, 5, 6, 6, 6, 15, 15, 15, 6, 6, 4, 5, 5, 5, 5, 15, 15, 23, 23, 15, 23, 23, 5, 5, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463530253 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 Building ZINC001463530253 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001463530253 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 778) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463530253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530253 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 13, 21, 21, 13, 21, 21, 4, 6, 6, 6, 12, 12, 12, 6, 6, 3, 4, 4, 4, 4, 13, 13, 21, 21, 13, 21, 21, 4, 4, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 779) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463530253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530253 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 15, 23, 23, 15, 23, 23, 5, 6, 6, 6, 15, 15, 15, 6, 6, 4, 5, 5, 5, 5, 15, 15, 23, 23, 15, 23, 23, 5, 5, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 780) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530253.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001463530253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530253 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 13, 21, 21, 13, 21, 21, 4, 6, 6, 6, 12, 12, 12, 6, 6, 3, 4, 4, 4, 4, 13, 13, 21, 21, 13, 21, 21, 4, 4, 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 781) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530253.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001463530253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530253 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 6, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 15, 23, 23, 15, 23, 23, 5, 6, 6, 6, 15, 15, 15, 6, 6, 4, 5, 5, 5, 5, 15, 15, 23, 23, 15, 23, 23, 5, 5, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463530253 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530253 Building ZINC001463530272 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001463530272 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/782 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463530272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530272 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 14, 22, 22, 14, 22, 22, 5, 6, 6, 6, 16, 16, 16, 6, 6, 4, 5, 5, 5, 5, 14, 14, 22, 22, 14, 22, 22, 5, 5, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/783 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463530272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530272 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 13, 20, 20, 13, 20, 20, 4, 6, 6, 6, 12, 12, 12, 6, 6, 3, 4, 4, 4, 4, 13, 13, 20, 20, 13, 20, 20, 4, 4, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/784 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/784' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530272.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001463530272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530272 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 14, 22, 22, 14, 22, 22, 5, 6, 6, 6, 16, 16, 16, 6, 6, 4, 5, 5, 5, 5, 14, 14, 22, 22, 14, 22, 22, 5, 5, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/785 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/785' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530272.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001463530272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530272 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 13, 20, 20, 13, 20, 20, 4, 6, 6, 6, 12, 12, 12, 6, 6, 3, 4, 4, 4, 4, 13, 13, 20, 20, 13, 20, 20, 4, 4, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463530272 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 Building ZINC001463530272 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001463530272 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 782) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463530272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530272 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 14, 22, 22, 14, 22, 22, 5, 6, 6, 6, 16, 16, 16, 6, 6, 4, 5, 5, 5, 5, 14, 14, 22, 22, 14, 22, 22, 5, 5, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 783) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463530272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530272 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 13, 20, 20, 13, 20, 20, 4, 6, 6, 6, 12, 12, 12, 6, 6, 3, 4, 4, 4, 4, 13, 13, 20, 20, 13, 20, 20, 4, 4, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 784) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530272.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001463530272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530272 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 14, 22, 22, 14, 22, 22, 5, 6, 6, 6, 16, 16, 16, 6, 6, 4, 5, 5, 5, 5, 14, 14, 22, 22, 14, 22, 22, 5, 5, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 785) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530272.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001463530272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530272 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 13, 20, 20, 13, 20, 20, 4, 6, 6, 6, 12, 12, 12, 6, 6, 3, 4, 4, 4, 4, 13, 13, 20, 20, 13, 20, 20, 4, 4, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463530272 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 Building ZINC001463530272 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001463530272 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 782) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463530272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530272 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 14, 22, 22, 14, 22, 22, 5, 6, 6, 6, 16, 16, 16, 6, 6, 4, 5, 5, 5, 5, 14, 14, 22, 22, 14, 22, 22, 5, 5, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 783) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463530272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530272 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 13, 20, 20, 13, 20, 20, 4, 6, 6, 6, 12, 12, 12, 6, 6, 3, 4, 4, 4, 4, 13, 13, 20, 20, 13, 20, 20, 4, 4, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 784) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530272.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001463530272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530272 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 14, 22, 22, 14, 22, 22, 5, 6, 6, 6, 16, 16, 16, 6, 6, 4, 5, 5, 5, 5, 14, 14, 22, 22, 14, 22, 22, 5, 5, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 785) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530272.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001463530272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530272 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 13, 20, 20, 13, 20, 20, 4, 6, 6, 6, 12, 12, 12, 6, 6, 3, 4, 4, 4, 4, 13, 13, 20, 20, 13, 20, 20, 4, 4, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463530272 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 Building ZINC001463530272 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001463530272 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 782) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463530272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530272 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 14, 22, 22, 14, 22, 22, 5, 6, 6, 6, 16, 16, 16, 6, 6, 4, 5, 5, 5, 5, 14, 14, 22, 22, 14, 22, 22, 5, 5, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 783) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463530272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530272 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 13, 20, 20, 13, 20, 20, 4, 6, 6, 6, 12, 12, 12, 6, 6, 3, 4, 4, 4, 4, 13, 13, 20, 20, 13, 20, 20, 4, 4, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 784) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530272.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001463530272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530272 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 14, 22, 22, 14, 22, 22, 5, 6, 6, 6, 16, 16, 16, 6, 6, 4, 5, 5, 5, 5, 14, 14, 22, 22, 14, 22, 22, 5, 5, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 785) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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@]2(C(F)(F)F)CCN(Cc3ccccc3)C2)cc1Cl) `ZINC001463530272.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001463530272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001463530272 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@]2(C(F)(F)F)CCN(Cc3ccccc3)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', 'F', 'F', 'F', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 15, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 1, 1, 16, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 13, 20, 20, 13, 20, 20, 4, 6, 6, 6, 12, 12, 12, 6, 6, 3, 4, 4, 4, 4, 13, 13, 20, 20, 13, 20, 20, 4, 4, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463530272 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463530272 Building ZINC001463581634 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463581634 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/786 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c2)cc1) `ZINC001463581634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463581634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001463581634 none CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 10, 18, 18, 10, 6, 4, 6, 6, 4, 4, 4, 4, 4, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 18, 18, 22, 22, 22, 22, 22, 18, 18, 10, 4, 4, 5, 5, 5, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 18, 18] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/787 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c2)cc1) `ZINC001463581634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463581634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001463581634 none CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 10, 18, 18, 10, 6, 4, 6, 6, 4, 4, 4, 4, 4, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 18, 18, 22, 22, 22, 22, 22, 18, 18, 10, 4, 4, 5, 5, 5, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 18, 18] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463581634 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634 Building ZINC001463581634 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463581634 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 786) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c2)cc1) `ZINC001463581634.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463581634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001463581634 none CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@]([O-])([SiH3])C(C)(C)CC)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 10, 18, 18, 10, 6, 4, 6, 6, 4, 4, 4, 4, 4, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 18, 18, 22, 22, 22, 22, 22, 18, 18, 10, 4, 4, 5, 5, 5, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 18, 18] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 787) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c2)cc1) `ZINC001463581634.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463581634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001463581634 none CCOc1ccc(NS(=O)(=O)c2ccc(OC)c(NC(=O)[C@@]([O-])([SiH3])C(C)(C)CC)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 10, 18, 18, 10, 6, 4, 6, 6, 4, 4, 4, 4, 4, 5, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 18, 18, 22, 22, 22, 22, 22, 18, 18, 10, 4, 4, 5, 5, 5, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 18, 18] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463581634 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463581634 Building ZINC001463590555 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463590555 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/788 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(NS(=O)(=O)c2ccc3c(c2)OCCCO3)cc1) `ZINC001463590555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463590555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001463590555 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(NS(=O)(=O)c2ccc3c(c2)OCCCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 8, 9, 9, 9, 17, 22, 22, 22, 17, 22, 22, 22, 22, 22, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 2, 2] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 42] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/789 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(NS(=O)(=O)c2ccc3c(c2)OCCCO3)cc1) `ZINC001463590555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463590555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001463590555 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(NS(=O)(=O)c2ccc3c(c2)OCCCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 8, 9, 9, 9, 17, 22, 22, 22, 17, 22, 22, 22, 22, 22, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 2, 2] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 42] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463590555 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555 Building ZINC001463590555 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463590555 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 788) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(NS(=O)(=O)c2ccc3c(c2)OCCCO3)cc1) `ZINC001463590555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463590555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001463590555 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)Nc1ccc(NS(=O)(=O)c2ccc3c(c2)OCCCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 8, 9, 9, 9, 17, 22, 22, 22, 17, 22, 22, 22, 22, 22, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 2, 2] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 42] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 789) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(NS(=O)(=O)c2ccc3c(c2)OCCCO3)cc1) `ZINC001463590555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463590555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001463590555 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)Nc1ccc(NS(=O)(=O)c2ccc3c(c2)OCCCO3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 6, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 8, 9, 9, 9, 17, 22, 22, 22, 17, 22, 22, 22, 22, 22, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 2, 2] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 42] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463590555 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463590555 Building ZINC001463652646 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463652646 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/790 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(S(=O)(=O)Nc2ccc(Cl)cc2)cc1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001463652646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463652646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001463652646 none O=C(Nc1ccc(S(=O)(=O)Nc2ccc(Cl)cc2)cc1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 8, 8, 3, 3, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 8, 8, 50, 50, 50, 50, 50, 8, 8, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/791 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(S(=O)(=O)Nc2ccc(Cl)cc2)cc1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001463652646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463652646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001463652646 none O=C(Nc1ccc(S(=O)(=O)Nc2ccc(Cl)cc2)cc1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 8, 8, 5, 8, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 8, 8, 50, 50, 50, 50, 50, 8, 8, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463652646 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646 Building ZINC001463652646 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463652646 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 790) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(S(=O)(=O)Nc2ccc(Cl)cc2)cc1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001463652646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463652646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001463652646 none O=C(Nc1ccc(S(=O)(=O)Nc2ccc(Cl)cc2)cc1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 8, 8, 3, 3, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 8, 8, 50, 50, 50, 50, 50, 8, 8, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 791) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(S(=O)(=O)Nc2ccc(Cl)cc2)cc1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001463652646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463652646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001463652646 none O=C(Nc1ccc(S(=O)(=O)Nc2ccc(Cl)cc2)cc1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', '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, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 8, 8, 5, 8, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 8, 8, 50, 50, 50, 50, 50, 8, 8, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463652646 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463652646 Building ZINC001463864135 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463864135 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/792 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001463864135.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463864135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001463864135 none O=C(Nc1ccccc1)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 47, 47, 47, 47, 47, 47, 23, 23, 23, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 23, 23, 47, 47, 47, 47, 47, 47, 23, 23, 23, 23, 22, 2, 4, 4, 23, 23, 23, 23] 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]) total number of confs: 151 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/793 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccccc1)N1CCC(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001463864135.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463864135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001463864135 none O=C(Nc1ccccc1)N1CCC(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 47, 47, 47, 47, 47, 47, 23, 23, 23, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 23, 23, 47, 47, 47, 47, 47, 47, 23, 23, 23, 23, 22, 2, 4, 4, 23, 23, 23, 23] 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]) total number of confs: 150 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463864135 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135 Building ZINC001463864135 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463864135 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 792) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccccc1)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001463864135.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463864135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001463864135 none O=C(Nc1ccccc1)N1CCC(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 47, 47, 47, 47, 47, 47, 23, 23, 23, 5, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 23, 23, 47, 47, 47, 47, 47, 47, 23, 23, 23, 23, 22, 2, 4, 4, 23, 23, 23, 23] 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]) total number of confs: 151 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 793) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccccc1)N1CCC(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001463864135.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463864135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001463864135 none O=C(Nc1ccccc1)N1CCC(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', '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, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 47, 47, 47, 47, 47, 47, 23, 23, 23, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 23, 23, 47, 47, 47, 47, 47, 47, 23, 23, 23, 23, 22, 2, 4, 4, 23, 23, 23, 23] 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]) total number of confs: 150 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463864135 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463864135 Building ZINC001463953382 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463953382 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/794 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC(=O)Nc1ccc(F)c(F)c1F)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001463953382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463953382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001463953382 none CCCN(CC(=O)Nc1ccc(F)c(F)c1F)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 3, 2, 3, 8, 14, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 8, 8, 14, 26, 26, 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]) total number of confs: 98 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/795 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC(=O)Nc1ccc(F)c(F)c1F)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001463953382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463953382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001463953382 none CCCN(CC(=O)Nc1ccc(F)c(F)c1F)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 3, 4, 9, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 9, 9, 16, 28, 28, 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]) total number of confs: 95 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463953382 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382 Building ZINC001463953382 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463953382 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 794) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC(=O)Nc1ccc(F)c(F)c1F)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001463953382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463953382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001463953382 none CCCN(CC(=O)Nc1ccc(F)c(F)c1F)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 3, 2, 3, 8, 14, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 8, 8, 14, 26, 26, 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]) total number of confs: 98 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 795) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC(=O)Nc1ccc(F)c(F)c1F)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001463953382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463953382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001463953382 none CCCN(CC(=O)Nc1ccc(F)c(F)c1F)C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 3, 4, 9, 16, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 9, 9, 16, 28, 28, 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]) total number of confs: 95 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463953382 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463953382 Building ZINC001463983861 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463983861 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/796 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccc(Cl)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001463983861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463983861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001463983861 none O=C(c1ccc(Cl)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 44, 47, 47, 46, 46, 47, 47, 18, 18, 18, 5, 2, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 18, 47, 47, 47, 47, 18, 18, 18, 18, 3, 1, 3, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/797 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccc(Cl)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001463983861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463983861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001463983861 none O=C(c1ccc(Cl)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 46, 48, 48, 48, 48, 48, 48, 19, 19, 19, 6, 2, 10, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 19, 19, 48, 48, 48, 48, 19, 19, 19, 19, 3, 1, 3, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463983861 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861 Building ZINC001463983861 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463983861 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 796) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(c1ccc(Cl)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001463983861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463983861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001463983861 none O=C(c1ccc(Cl)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 44, 47, 47, 46, 46, 47, 47, 18, 18, 18, 5, 2, 9, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 18, 47, 47, 47, 47, 18, 18, 18, 18, 3, 1, 3, 18, 18, 18, 18] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 797) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(c1ccc(Cl)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001463983861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463983861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001463983861 none O=C(c1ccc(Cl)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 46, 48, 48, 48, 48, 48, 48, 19, 19, 19, 6, 2, 10, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 19, 19, 48, 48, 48, 48, 19, 19, 19, 19, 3, 1, 3, 19, 19, 19, 19] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463983861 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463983861 Building ZINC001463995150 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463995150 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/798 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nnc(CCCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n1C1CCCC1) `ZINC001463995150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463995150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001463995150 none CSc1nnc(CCCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n1C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', '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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 27, 27, 27, 27, 16, 12, 13, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 30, 30, 30, 30, 30, 31, 31, 31, 15, 16, 15, 15, 13, 13, 4, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/799 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nnc(CCCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n1C1CCCC1) `ZINC001463995150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463995150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001463995150 none CSc1nnc(CCCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n1C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', '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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 29, 29, 29, 29, 17, 13, 13, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 30, 30, 30, 30, 33, 33, 33, 16, 17, 16, 16, 13, 13, 4, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463995150 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150 Building ZINC001463995150 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001463995150 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 798) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nnc(CCCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n1C1CCCC1) `ZINC001463995150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001463995150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001463995150 none CSc1nnc(CCCNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n1C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', '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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 27, 27, 27, 27, 16, 12, 13, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 27, 30, 30, 30, 30, 30, 31, 31, 31, 15, 16, 15, 15, 13, 13, 4, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 799) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nnc(CCCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n1C1CCCC1) `ZINC001463995150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001463995150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001463995150 none CSc1nnc(CCCNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)n1C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', '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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 29, 29, 29, 29, 17, 13, 13, 4, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 29, 29, 30, 30, 30, 30, 33, 33, 33, 16, 17, 16, 16, 13, 13, 4, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001463995150 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001463995150 Building ZINC001464120714 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464120714 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/800 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2cccc(C(F)(F)F)c2)CC1) `ZINC001464120714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464120714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001464120714 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2cccc(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 4, 4, 6, 6, 6, 6, 17, 17, 17, 17, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/801 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2cccc(C(F)(F)F)c2)CC1) `ZINC001464120714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464120714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001464120714 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2cccc(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 5, 5, 5, 5, 17, 17, 5, 17, 17, 17, 17, 17, 17, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 17, 17, 5, 17, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/802 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/802' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2cccc(C(F)(F)F)c2)CC1) `ZINC001464120714.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464120714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001464120714 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2cccc(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 4, 4, 6, 6, 6, 6, 17, 17, 17, 17, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/803 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/803' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2cccc(C(F)(F)F)c2)CC1) `ZINC001464120714.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464120714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001464120714 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2cccc(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 18, 18, 18, 18, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464120714 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 Building ZINC001464120714 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464120714 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 800) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2cccc(C(F)(F)F)c2)CC1) `ZINC001464120714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464120714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001464120714 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2cccc(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 4, 4, 6, 6, 6, 6, 17, 17, 17, 17, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 801) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2cccc(C(F)(F)F)c2)CC1) `ZINC001464120714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464120714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001464120714 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2cccc(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 5, 5, 5, 5, 17, 17, 5, 17, 17, 17, 17, 17, 17, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 17, 17, 5, 17, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 802) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2cccc(C(F)(F)F)c2)CC1) `ZINC001464120714.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464120714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001464120714 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2cccc(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 4, 4, 6, 6, 6, 6, 17, 17, 17, 17, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 803) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2cccc(C(F)(F)F)c2)CC1) `ZINC001464120714.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464120714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001464120714 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2cccc(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 18, 18, 18, 18, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464120714 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 Building ZINC001464120714 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464120714 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 800) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2cccc(C(F)(F)F)c2)CC1) `ZINC001464120714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464120714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001464120714 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2cccc(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 4, 4, 6, 6, 6, 6, 17, 17, 17, 17, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 801) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2cccc(C(F)(F)F)c2)CC1) `ZINC001464120714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464120714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001464120714 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2cccc(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 5, 5, 5, 5, 17, 17, 5, 17, 17, 17, 17, 17, 17, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 17, 17, 5, 17, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 802) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2cccc(C(F)(F)F)c2)CC1) `ZINC001464120714.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464120714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001464120714 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2cccc(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 4, 4, 6, 6, 6, 6, 17, 17, 17, 17, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 803) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2cccc(C(F)(F)F)c2)CC1) `ZINC001464120714.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464120714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001464120714 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2cccc(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 18, 18, 18, 18, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464120714 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 Building ZINC001464120714 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001464120714 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 800) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2cccc(C(F)(F)F)c2)CC1) `ZINC001464120714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464120714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001464120714 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2cccc(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 4, 4, 6, 6, 6, 6, 17, 17, 17, 17, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 801) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2cccc(C(F)(F)F)c2)CC1) `ZINC001464120714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464120714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001464120714 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@](c2cccc(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 5, 5, 5, 5, 17, 17, 5, 17, 17, 17, 17, 17, 17, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 17, 17, 5, 17, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 802) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2cccc(C(F)(F)F)c2)CC1) `ZINC001464120714.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001464120714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001464120714 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2cccc(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 4, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 4, 4, 6, 6, 6, 6, 17, 17, 17, 17, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 803) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2cccc(C(F)(F)F)c2)CC1) `ZINC001464120714.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001464120714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001464120714 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCC[N@]1CC[N@@](c2cccc(C(F)(F)F)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 18, 18, 18, 18, 5, 5, 5, 5] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 41] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464120714 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464120714 Building ZINC001464262845 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464262845 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/804 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(F)cc1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001464262845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464262845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001464262845 none O=C(NCc1ccc(F)cc1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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: [17, 4, 17, 17, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 4, 17, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 2, 2, 2, 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]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/805 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(F)cc1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001464262845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464262845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001464262845 none O=C(NCc1ccc(F)cc1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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: [20, 8, 20, 20, 49, 49, 49, 49, 49, 49, 49, 8, 8, 8, 3, 2, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 20, 49, 49, 49, 49, 49, 49, 8, 8, 8, 8, 8, 3, 1, 3, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 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]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464262845 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845 Building ZINC001464262845 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464262845 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 804) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCc1ccc(F)cc1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001464262845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464262845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001464262845 none O=C(NCc1ccc(F)cc1)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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: [17, 4, 17, 17, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 4, 17, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 2, 2, 2, 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]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 805) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCc1ccc(F)cc1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001464262845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464262845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001464262845 none O=C(NCc1ccc(F)cc1)C1CCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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: [20, 8, 20, 20, 49, 49, 49, 49, 49, 49, 49, 8, 8, 8, 3, 2, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 8, 8, 20, 49, 49, 49, 49, 49, 49, 8, 8, 8, 8, 8, 3, 1, 3, 8, 8, 8, 8] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 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]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464262845 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464262845 Building ZINC001464298207 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464298207 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/806 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCCOc2ccccc2)nc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464298207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464298207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001464298207 none O=C(NCc1ccc(OCCOc2ccccc2)nc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 16, 16, 16, 16, 16, 19, 19, 36, 36, 36, 36, 36, 36, 16, 16, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 16, 16, 19, 19, 19, 19, 36, 36, 36, 36, 36, 16, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 33, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/807 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc(OCCOc2ccccc2)nc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464298207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464298207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001464298207 none O=C(NCc1ccc(OCCOc2ccccc2)nc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 16, 16, 16, 16, 16, 19, 19, 36, 36, 36, 36, 36, 36, 16, 16, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 16, 16, 19, 19, 19, 19, 36, 36, 36, 36, 36, 16, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 33, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464298207 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207 Building ZINC001464298207 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464298207 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 806) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCc1ccc(OCCOc2ccccc2)nc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464298207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464298207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001464298207 none O=C(NCc1ccc(OCCOc2ccccc2)nc1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 16, 16, 16, 16, 16, 19, 19, 36, 36, 36, 36, 36, 36, 16, 16, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 16, 16, 19, 19, 19, 19, 36, 36, 36, 36, 36, 16, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 33, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 807) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCc1ccc(OCCOc2ccccc2)nc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464298207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464298207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001464298207 none O=C(NCc1ccc(OCCOc2ccccc2)nc1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 3, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 16, 16, 16, 16, 16, 19, 19, 36, 36, 36, 36, 36, 36, 16, 16, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 6, 6, 16, 16, 19, 19, 19, 19, 36, 36, 36, 36, 36, 16, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 33, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464298207 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464298207 Building ZINC001464331737 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464331737 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/808 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccccc2OC)N2CCCCC2)cc1Cl) `ZINC001464331737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464331737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001464331737 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccccc2OC)N2CCCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 7, 13, 13, 18, 18, 18, 18, 18, 18, 20, 15, 18, 18, 18, 18, 18, 6, 6, 6, 13, 13, 13, 6, 6, 3, 7, 7, 18, 18, 18, 18, 20, 20, 20, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 107 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/809 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccccc2OC)N2CCCCC2)cc1Cl) `ZINC001464331737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464331737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001464331737 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccccc2OC)N2CCCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 14, 14, 18, 18, 17, 18, 18, 18, 21, 16, 20, 20, 20, 20, 20, 5, 5, 5, 12, 12, 12, 5, 5, 2, 6, 6, 18, 18, 18, 18, 21, 21, 21, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 116 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464331737 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737 Building ZINC001464331737 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464331737 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 808) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccccc2OC)N2CCCCC2)cc1Cl) `ZINC001464331737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464331737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001464331737 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H](c2ccccc2OC)N2CCCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 7, 13, 13, 18, 18, 18, 18, 18, 18, 20, 15, 18, 18, 18, 18, 18, 6, 6, 6, 13, 13, 13, 6, 6, 3, 7, 7, 18, 18, 18, 18, 20, 20, 20, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 107 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 809) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccccc2OC)N2CCCCC2)cc1Cl) `ZINC001464331737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464331737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001464331737 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H](c2ccccc2OC)N2CCCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 14, 14, 18, 18, 17, 18, 18, 18, 21, 16, 20, 20, 20, 20, 20, 5, 5, 5, 12, 12, 12, 5, 5, 2, 6, 6, 18, 18, 18, 18, 21, 21, 21, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 116 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464331737 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331737 Building ZINC001464331740 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464331740 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/810 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccccc2OC)N2CCCCC2)cc1Cl) `ZINC001464331740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464331740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001464331740 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccccc2OC)N2CCCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 18, 18, 18, 18, 18, 18, 21, 17, 20, 20, 20, 20, 20, 5, 5, 5, 12, 12, 12, 5, 5, 2, 7, 7, 18, 18, 18, 18, 21, 21, 21, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 110 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/811 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccccc2OC)N2CCCCC2)cc1Cl) `ZINC001464331740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464331740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001464331740 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccccc2OC)N2CCCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 7, 13, 13, 18, 18, 18, 18, 18, 18, 20, 15, 18, 18, 18, 18, 18, 6, 6, 6, 13, 13, 13, 6, 6, 3, 7, 7, 18, 18, 18, 18, 20, 20, 20, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 107 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464331740 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740 Building ZINC001464331740 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464331740 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 810) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccccc2OC)N2CCCCC2)cc1Cl) `ZINC001464331740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464331740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001464331740 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H](c2ccccc2OC)N2CCCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 18, 18, 18, 18, 18, 18, 21, 17, 20, 20, 20, 20, 20, 5, 5, 5, 12, 12, 12, 5, 5, 2, 7, 7, 18, 18, 18, 18, 21, 21, 21, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 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]) total number of confs: 110 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 811) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccccc2OC)N2CCCCC2)cc1Cl) `ZINC001464331740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464331740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001464331740 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H](c2ccccc2OC)N2CCCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.3', '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', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 10, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 3, 7, 13, 13, 18, 18, 18, 18, 18, 18, 20, 15, 18, 18, 18, 18, 18, 6, 6, 6, 13, 13, 13, 6, 6, 3, 7, 7, 18, 18, 18, 18, 20, 20, 20, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 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]) total number of confs: 107 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464331740 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464331740 Building ZINC001464341840 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464341840 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/812 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCOCC2)cc1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464341840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464341840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001464341840 none O=C(Nc1ccc(N2CCOCC2)cc1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 4, 6, 27, 27, 27, 27, 26, 7, 7, 7, 7, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 7, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/813 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(N2CCOCC2)cc1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464341840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464341840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001464341840 none O=C(Nc1ccc(N2CCOCC2)cc1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 4, 6, 28, 28, 28, 28, 26, 7, 7, 7, 7, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 7, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464341840 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840 Building ZINC001464341840 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464341840 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 812) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(N2CCOCC2)cc1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464341840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464341840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001464341840 none O=C(Nc1ccc(N2CCOCC2)cc1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 4, 6, 27, 27, 27, 27, 26, 7, 7, 7, 7, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 7, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 813) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(N2CCOCC2)cc1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001464341840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464341840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001464341840 none O=C(Nc1ccc(N2CCOCC2)cc1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 7, 4, 6, 28, 28, 28, 28, 26, 7, 7, 7, 7, 7, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 7, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464341840 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464341840 Building ZINC001464419386 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464419386 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/814 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1)C(=O)OC(C)(C)C) `ZINC001464419386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464419386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001464419386 none CN(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 5, 5, 5, 5, 5, 5, 3, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 5, 18, 25, 25, 34, 34, 34, 34, 18, 18, 18, 13, 13, 5, 5, 5, 5, 5, 5, 2, 2, 5, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/815 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1)C(=O)OC(C)(C)C) `ZINC001464419386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464419386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001464419386 none CN(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 6, 6, 6, 6, 6, 6, 4, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 6, 18, 25, 25, 33, 33, 33, 33, 18, 18, 18, 13, 13, 6, 6, 6, 6, 6, 6, 2, 2, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464419386 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386 Building ZINC001464419386 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464419386 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 814) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1)C(=O)OC(C)(C)C) `ZINC001464419386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464419386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001464419386 none CN(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 5, 5, 5, 5, 5, 5, 3, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 5, 18, 25, 25, 34, 34, 34, 34, 18, 18, 18, 13, 13, 5, 5, 5, 5, 5, 5, 2, 2, 5, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 815) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CN(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1)C(=O)OC(C)(C)C) `ZINC001464419386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464419386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001464419386 none CN(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 13, 6, 6, 6, 6, 6, 6, 4, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 6, 18, 25, 25, 33, 33, 33, 33, 18, 18, 18, 13, 13, 6, 6, 6, 6, 6, 6, 2, 2, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464419386 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419386 Building ZINC001464419392 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464419392 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/816 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1)C(=O)OC(C)(C)C) `ZINC001464419392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464419392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001464419392 none CN(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 5, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 7, 19, 27, 27, 36, 36, 36, 36, 19, 19, 19, 14, 14, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 121 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/817 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1)C(=O)OC(C)(C)C) `ZINC001464419392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464419392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001464419392 none CN(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 13, 5, 5, 5, 5, 5, 5, 3, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 5, 20, 28, 28, 37, 37, 37, 37, 20, 20, 20, 13, 13, 5, 5, 5, 5, 5, 5, 2, 2, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 125 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464419392 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392 Building ZINC001464419392 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464419392 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 816) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/816: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1)C(=O)OC(C)(C)C) `ZINC001464419392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464419392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001464419392 none CN(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 7, 7, 7, 7, 7, 5, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 7, 19, 27, 27, 36, 36, 36, 36, 19, 19, 19, 14, 14, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 121 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 817) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1)C(=O)OC(C)(C)C) `ZINC001464419392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464419392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001464419392 none CN(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.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, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 13, 5, 5, 5, 5, 5, 5, 3, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 5, 20, 28, 28, 37, 37, 37, 37, 20, 20, 20, 13, 13, 5, 5, 5, 5, 5, 5, 2, 2, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 125 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464419392 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464419392 Building ZINC001464439813 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464439813 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/818 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccc(Cl)cc1)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464439813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464439813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001464439813 none O=C(c1ccc(Cl)cc1)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 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, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 34, 35, 35, 34, 35, 35, 35, 15, 15, 15, 15, 11, 1, 12, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 35, 35, 35, 35, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 15, 15, 15, 15] 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: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/819 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccc(Cl)cc1)N1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464439813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464439813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001464439813 none O=C(c1ccc(Cl)cc1)N1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 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, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 10, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 29, 29, 29, 29, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 14, 14, 14, 14] 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: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464439813 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813 Building ZINC001464439813 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464439813 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 818) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(c1ccc(Cl)cc1)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464439813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464439813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001464439813 none O=C(c1ccc(Cl)cc1)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 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, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 34, 35, 35, 34, 35, 35, 35, 15, 15, 15, 15, 11, 1, 12, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 35, 35, 35, 35, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3, 15, 15, 15, 15] 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: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 819) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(c1ccc(Cl)cc1)N1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464439813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464439813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001464439813 none O=C(c1ccc(Cl)cc1)N1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 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, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 10, 1, 10, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 29, 29, 29, 29, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 14, 14, 14, 14] 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: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464439813 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464439813 Building ZINC001464555630 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464555630 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/820 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1NC(=O)CN1CCCCC1) `ZINC001464555630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464555630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001464555630 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1NC(=O)CN1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 13, 13, 13, 36, 36, 36, 36, 36, 36, 11, 11, 11, 11, 11, 3, 4, 4, 4, 4, 11, 13, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/821 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1NC(=O)CN1CCCCC1) `ZINC001464555630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464555630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001464555630 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1NC(=O)CN1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 12, 12, 12, 35, 35, 35, 35, 35, 35, 10, 10, 10, 10, 10, 3, 4, 4, 4, 4, 10, 12, 35, 35, 35, 35, 35, 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, 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/6899/xaj-8058088.10/working/building/ZINC001464555630 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464555630 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630 Building ZINC001464555630 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464555630 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 820) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1NC(=O)CN1CCCCC1) `ZINC001464555630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464555630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001464555630 none Cc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1NC(=O)CN1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 13, 13, 13, 36, 36, 36, 36, 36, 36, 11, 11, 11, 11, 11, 3, 4, 4, 4, 4, 11, 13, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 821) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1NC(=O)CN1CCCCC1) `ZINC001464555630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464555630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001464555630 none Cc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1NC(=O)CN1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 12, 12, 12, 35, 35, 35, 35, 35, 35, 10, 10, 10, 10, 10, 3, 4, 4, 4, 4, 10, 12, 35, 35, 35, 35, 35, 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, 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/6899/xaj-8058088.10/working/building/ZINC001464555630 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464555630 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464555630 Building ZINC001464615834 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464615834 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/822 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(OC)c1OC1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464615834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464615834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464615834 none COc1cccc(OC)c1OC1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 23, 24, 16, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 23, 23, 23, 24, 24, 24, 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, 50, 51, 52, 53]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/823 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(OC)c1OC1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464615834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464615834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464615834 none COc1cccc(OC)c1OC1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 27, 27, 27, 27, 27, 27, 30, 16, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 27, 27, 27, 30, 30, 30, 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, 50, 51, 52, 53]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464615834 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834 Building ZINC001464615834 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464615834 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 822) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1cccc(OC)c1OC1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464615834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464615834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464615834 none COc1cccc(OC)c1OC1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 23, 23, 24, 16, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 24, 24, 24, 23, 23, 23, 24, 24, 24, 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, 50, 51, 52, 53]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 823) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1cccc(OC)c1OC1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1) `ZINC001464615834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464615834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464615834 none COc1cccc(OC)c1OC1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 27, 27, 27, 27, 27, 27, 30, 16, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 27, 27, 27, 30, 30, 30, 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, 50, 51, 52, 53]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464615834 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464615834 Building ZINC001464677224 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464677224 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/824 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2n[nH]c(c3ccccc3)n2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001464677224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464677224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001464677224 none O=C(N1CCC(c2n[nH]c(c3ccccc3)n2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 4, 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] 0 hydrogens need 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, 4, 5, 5, 5, 5, 33, 33, 33, 33, 33, 36, 36, 33, 36, 36, 33, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 36, 36, 33, 36, 36, 5, 5, 5, 5, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/825 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2n[nH]c(c3ccccc3)n2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001464677224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464677224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001464677224 none O=C(N1CCC(c2n[nH]c(c3ccccc3)n2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 4, 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] 0 hydrogens need 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, 4, 5, 5, 5, 5, 40, 40, 40, 40, 40, 42, 42, 40, 42, 42, 40, 5, 5, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 42, 42, 40, 42, 42, 5, 5, 5, 5, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464677224 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224 Building ZINC001464677224 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464677224 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 824) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2n[nH]c(c3ccccc3)n2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001464677224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464677224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001464677224 none O=C(N1CCC(c2n[nH]c(c3ccccc3)n2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 4, 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] 0 hydrogens need 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, 4, 5, 5, 5, 5, 33, 33, 33, 33, 33, 36, 36, 33, 36, 36, 33, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 36, 36, 33, 36, 36, 5, 5, 5, 5, 4, 4] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 825) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(c2n[nH]c(c3ccccc3)n2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001464677224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464677224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001464677224 none O=C(N1CCC(c2n[nH]c(c3ccccc3)n2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 4, 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] 0 hydrogens need 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, 4, 5, 5, 5, 5, 40, 40, 40, 40, 40, 42, 42, 40, 42, 42, 40, 5, 5, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 42, 42, 40, 42, 42, 5, 5, 5, 5, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464677224 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464677224 Building ZINC001464702307 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464702307 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/826 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(Cc2cnc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)s2)c1) `ZINC001464702307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464702307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001464702307 none COC(=O)c1cccc(Cc2cnc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)s2)c1 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.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', '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, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 14, 1, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 26, 16, 16, 16, 16, 8, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 16, 26, 26, 26, 16, 16, 16, 8, 8, 4, 2, 3, 3, 3, 3, 16] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/827 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cccc(Cc2cnc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)s2)c1) `ZINC001464702307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464702307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001464702307 none COC(=O)c1cccc(Cc2cnc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)s2)c1 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.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', '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, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 14, 1, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 26, 16, 16, 16, 16, 8, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 16, 26, 26, 26, 16, 16, 16, 8, 8, 4, 2, 3, 3, 3, 3, 16] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464702307 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307 Building ZINC001464702307 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464702307 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 826) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)c1cccc(Cc2cnc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)s2)c1) `ZINC001464702307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464702307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001464702307 none COC(=O)c1cccc(Cc2cnc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)s2)c1 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.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', '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, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 14, 1, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 26, 16, 16, 16, 16, 8, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 16, 26, 26, 26, 16, 16, 16, 8, 8, 4, 2, 3, 3, 3, 3, 16] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 827) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COC(=O)c1cccc(Cc2cnc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)s2)c1) `ZINC001464702307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464702307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001464702307 none COC(=O)c1cccc(Cc2cnc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)s2)c1 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.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', '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, 5, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 14, 1, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 26, 16, 16, 16, 16, 8, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 16, 26, 26, 26, 16, 16, 16, 8, 8, 4, 2, 3, 3, 3, 3, 16] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464702307 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464702307 Building ZINC001464811058 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464811058 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/828 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cn2ncc(C)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464811058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464811058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001464811058 none COc1ccc(Cn2ncc(C)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 21, 21, 21, 12, 8, 8, 8, 8, 8, 8, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 33, 34, 34, 34, 21, 21, 12, 12, 8, 8, 8, 8, 5, 4, 4, 4, 4, 21, 33, 33, 33] 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: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/829 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(Cn2ncc(C)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464811058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464811058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001464811058 none COc1ccc(Cn2ncc(C)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 21, 21, 21, 12, 8, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 34, 35, 35, 35, 21, 21, 12, 12, 8, 8, 8, 8, 4, 4, 4, 4, 4, 21, 34, 34, 34] 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: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464811058 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058 Building ZINC001464811058 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464811058 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 828) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cn2ncc(C)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464811058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464811058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001464811058 none COc1ccc(Cn2ncc(C)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 21, 21, 21, 12, 8, 8, 8, 8, 8, 8, 5, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 33, 34, 34, 34, 21, 21, 12, 12, 8, 8, 8, 8, 5, 4, 4, 4, 4, 21, 33, 33, 33] 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: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 829) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(Cn2ncc(C)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC) `ZINC001464811058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464811058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001464811058 none COc1ccc(Cn2ncc(C)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 8, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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] 0 hydrogens 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, 21, 21, 21, 12, 8, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 34, 35, 35, 35, 21, 21, 12, 12, 8, 8, 8, 8, 4, 4, 4, 4, 4, 21, 34, 34, 34] 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: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464811058 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464811058 Building ZINC001464812861 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464812861 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/830 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(NC(=O)[C@@H]2CSCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1C) `ZINC001464812861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464812861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464812861 none Cc1cccc(NC(=O)[C@@H]2CSCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 22, 37, 37, 21, 21, 9, 21, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 37, 37, 37, 37, 37, 32, 37, 37, 21, 9, 9, 9, 9, 5, 5, 5, 5, 37, 37, 37] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/831 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(NC(=O)[C@@H]2CSCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1C) `ZINC001464812861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464812861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464812861 none Cc1cccc(NC(=O)[C@@H]2CSCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 32, 32, 11, 11, 5, 11, 5, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 11, 32, 32, 11, 5, 5, 5, 5, 5, 5, 5, 5, 32, 32, 32] 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464812861 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861 Building ZINC001464812861 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464812861 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 830) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc(NC(=O)[C@@H]2CSCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1C) `ZINC001464812861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464812861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464812861 none Cc1cccc(NC(=O)[C@@H]2CSCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 22, 37, 37, 21, 21, 9, 21, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 37, 37, 37, 37, 37, 32, 37, 37, 21, 9, 9, 9, 9, 5, 5, 5, 5, 37, 37, 37] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 831) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc(NC(=O)[C@@H]2CSCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1C) `ZINC001464812861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464812861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464812861 none Cc1cccc(NC(=O)[C@@H]2CSCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 32, 32, 11, 11, 5, 11, 5, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 11, 32, 32, 11, 5, 5, 5, 5, 5, 5, 5, 5, 32, 32, 32] 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464812861 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812861 Building ZINC001464812870 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464812870 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/832 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(NC(=O)[C@H]2CSCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1C) `ZINC001464812870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464812870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464812870 none Cc1cccc(NC(=O)[C@H]2CSCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 31, 31, 12, 12, 5, 12, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 14, 31, 31, 12, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31] 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/833 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(NC(=O)[C@H]2CSCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1C) `ZINC001464812870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464812870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464812870 none Cc1cccc(NC(=O)[C@H]2CSCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 25, 25, 10, 25, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 25, 10, 10, 10, 10, 5, 5, 5, 5, 39, 39, 39] 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: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464812870 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870 Building ZINC001464812870 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464812870 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 832) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(NC(=O)[C@H]2CSCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1C) `ZINC001464812870.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464812870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464812870 none Cc1cccc(NC(=O)[C@H]2CSCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 31, 31, 12, 12, 5, 12, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 14, 31, 31, 12, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31] 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: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 833) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc(NC(=O)[C@H]2CSCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1C) `ZINC001464812870.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464812870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001464812870 none Cc1cccc(NC(=O)[C@H]2CSCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 5, 7, 7, 7, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 25, 25, 10, 25, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 39, 39, 39, 39, 39, 39, 39, 39, 25, 10, 10, 10, 10, 5, 5, 5, 5, 39, 39, 39] 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: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464812870 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464812870 Building ZINC001464988252 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464988252 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/834 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001464988252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464988252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001464988252 none CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 32, 32, 36, 36, 32, 36, 36, 36, 15, 15, 15, 6, 1, 3, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 15, 15, 37, 37, 37, 37, 37, 36, 36, 36, 36, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/835 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001464988252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464988252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001464988252 none CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 36, 15, 36, 36, 41, 41, 41, 41, 41, 41, 15, 15, 15, 7, 1, 4, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 15, 15, 44, 44, 44, 44, 44, 41, 41, 41, 41, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464988252 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252 Building ZINC001464988252 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464988252 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 834) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001464988252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464988252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001464988252 none CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 32, 32, 36, 36, 32, 36, 36, 36, 15, 15, 15, 6, 1, 3, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 15, 15, 37, 37, 37, 37, 37, 36, 36, 36, 36, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 175 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 835) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001464988252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464988252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001464988252 none CC[C@@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 36, 15, 36, 36, 41, 41, 41, 41, 41, 41, 15, 15, 15, 7, 1, 4, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 15, 15, 44, 44, 44, 44, 44, 41, 41, 41, 41, 15, 15, 15, 15, 4, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464988252 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988252 Building ZINC001464988258 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464988258 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/836 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001464988258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464988258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001464988258 none CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 15, 33, 33, 37, 37, 37, 37, 37, 37, 15, 15, 15, 6, 1, 3, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 15, 15, 38, 38, 38, 38, 38, 37, 37, 37, 37, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 159 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/837 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001464988258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464988258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001464988258 none CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 18, 34, 34, 38, 38, 38, 38, 38, 38, 18, 18, 18, 7, 1, 4, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 18, 18, 40, 40, 40, 40, 40, 38, 38, 38, 38, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464988258 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258 Building ZINC001464988258 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001464988258 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 836) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001464988258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001464988258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001464988258 none CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 15, 33, 33, 37, 37, 37, 37, 37, 37, 15, 15, 15, 6, 1, 3, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 15, 15, 38, 38, 38, 38, 38, 37, 37, 37, 37, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 159 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 837) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1) `ZINC001464988258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001464988258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001464988258 none CC[C@H](c1ccc(Br)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 1, 1, 1, 17, 1, 1, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 18, 34, 34, 38, 38, 38, 38, 38, 38, 18, 18, 18, 7, 1, 4, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5, 18, 18, 40, 40, 40, 40, 40, 38, 38, 38, 38, 18, 18, 18, 18, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001464988258 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001464988258 Building ZINC001465002061 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465002061 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/838 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)OC(C)(C)C)C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001465002061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465002061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465002061 none C[C@@H](NC(=O)OC(C)(C)C)C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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.2', 'C.2', 'Br', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 12, 12, 25, 33, 33, 39, 39, 39, 39, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 12, 12, 12, 25, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4, 4, 2, 2, 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, 50]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/839 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)OC(C)(C)C)C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001465002061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465002061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465002061 none C[C@@H](NC(=O)OC(C)(C)C)C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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.2', 'C.2', 'Br', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 16, 16, 27, 34, 34, 40, 40, 40, 40, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 16, 16, 16, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4, 4, 2, 2, 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, 50]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465002061 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061 Building ZINC001465002061 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465002061 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 838) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@@H](NC(=O)OC(C)(C)C)C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001465002061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465002061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465002061 none C[C@@H](NC(=O)OC(C)(C)C)C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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.2', 'C.2', 'Br', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 12, 12, 25, 33, 33, 39, 39, 39, 39, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 12, 12, 12, 25, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4, 4, 2, 2, 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, 50]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 839) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@@H](NC(=O)OC(C)(C)C)C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001465002061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465002061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465002061 none C[C@@H](NC(=O)OC(C)(C)C)C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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.2', 'C.2', 'Br', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 16, 16, 27, 34, 34, 40, 40, 40, 40, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 16, 16, 16, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4, 4, 2, 2, 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, 50]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465002061 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002061 Building ZINC001465002064 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465002064 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/840 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)OC(C)(C)C)C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001465002064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465002064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465002064 none C[C@H](NC(=O)OC(C)(C)C)C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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.2', 'C.2', 'Br', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 13, 13, 22, 31, 31, 37, 37, 37, 37, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 13, 13, 13, 22, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 2, 2, 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, 50]) total number of confs: 128 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/841 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)OC(C)(C)C)C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001465002064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465002064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465002064 none C[C@H](NC(=O)OC(C)(C)C)C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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.2', 'C.2', 'Br', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 15, 15, 24, 33, 33, 40, 40, 40, 40, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 15, 15, 15, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4, 4, 2, 2, 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, 50]) total number of confs: 134 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465002064 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064 Building ZINC001465002064 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465002064 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 840) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@H](NC(=O)OC(C)(C)C)C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001465002064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465002064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465002064 none C[C@H](NC(=O)OC(C)(C)C)C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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.2', 'C.2', 'Br', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 13, 13, 22, 31, 31, 37, 37, 37, 37, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 13, 13, 13, 22, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 2, 2, 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, 50]) total number of confs: 128 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 841) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@H](NC(=O)OC(C)(C)C)C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001465002064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465002064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465002064 none C[C@H](NC(=O)OC(C)(C)C)C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', '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.2', 'C.2', 'Br', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 15, 15, 24, 33, 33, 40, 40, 40, 40, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 15, 15, 15, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4, 4, 2, 2, 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, 50]) total number of confs: 134 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465002064 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465002064 Building ZINC001465037503 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465037503 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/842 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@](=O)C2CCOCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465037503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465037503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465037503 none O=C(Nc1cccc(C[S@](=O)C2CCOCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 3, 9, 9, 14, 22, 29, 31, 31, 31, 31, 31, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 9, 9, 3, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 9, 8, 8, 8, 8] 50 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, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/843 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@](=O)C2CCOCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465037503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465037503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465037503 none O=C(Nc1cccc(C[S@](=O)C2CCOCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 3, 9, 9, 15, 22, 29, 34, 34, 34, 34, 34, 9, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 9, 3, 15, 15, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 7, 7, 7, 7] 50 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, 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/6899/xaj-8058088.10/working/building/ZINC001465037503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465037503 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503 Building ZINC001465037503 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465037503 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 842) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1cccc(C[S@](=O)C2CCOCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465037503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465037503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465037503 none O=C(Nc1cccc(C[S@](=O)C2CCOCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 3, 9, 9, 14, 22, 29, 31, 31, 31, 31, 31, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 9, 9, 3, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 9, 8, 8, 8, 8] 50 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, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 843) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1cccc(C[S@](=O)C2CCOCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465037503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465037503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465037503 none O=C(Nc1cccc(C[S@](=O)C2CCOCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 3, 9, 9, 15, 22, 29, 34, 34, 34, 34, 34, 9, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 9, 3, 15, 15, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 7, 7, 7, 7] 50 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, 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/6899/xaj-8058088.10/working/building/ZINC001465037503 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465037503 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037503 Building ZINC001465037505 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465037505 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/844 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@@](=O)C2CCOCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465037505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465037505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465037505 none O=C(Nc1cccc(C[S@@](=O)C2CCOCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 3, 9, 9, 13, 21, 31, 35, 35, 35, 35, 35, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 9, 9, 3, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 9, 8, 8, 8, 8] 50 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, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/845 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(C[S@@](=O)C2CCOCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465037505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465037505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465037505 none O=C(Nc1cccc(C[S@@](=O)C2CCOCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 3, 9, 9, 13, 21, 31, 34, 34, 34, 34, 34, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 9, 9, 3, 13, 13, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 8, 8, 8, 8] 50 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, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465037505 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505 Building ZINC001465037505 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465037505 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 844) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(Nc1cccc(C[S@@](=O)C2CCOCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465037505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465037505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465037505 none O=C(Nc1cccc(C[S@@](=O)C2CCOCC2)c1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 3, 9, 9, 13, 21, 31, 35, 35, 35, 35, 35, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 9, 9, 3, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 35, 9, 8, 8, 8, 8] 50 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, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 845) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(Nc1cccc(C[S@@](=O)C2CCOCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465037505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465037505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465037505 none O=C(Nc1cccc(C[S@@](=O)C2CCOCC2)c1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 14, 11, 5, 5, 5, 12, 5, 5, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 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, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 3, 9, 9, 13, 21, 31, 34, 34, 34, 34, 34, 9, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 9, 9, 3, 13, 13, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 8, 8, 8, 8] 50 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, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465037505 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465037505 Building ZINC001465171652 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001465171652 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/846 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465171652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171652 none O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 36, 36, 36, 36, 12, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 12, 12, 12, 12, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/847 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465171652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171652 none O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 36, 36, 36, 36, 12, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 12, 12, 12, 12, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/848 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/848' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001465171652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171652 none O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 40, 40, 40, 40, 13, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/849 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/849' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001465171652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171652 none O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 40, 40, 40, 40, 13, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465171652 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 Building ZINC001465171652 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001465171652 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 846) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465171652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171652 none O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 36, 36, 36, 36, 12, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 12, 12, 12, 12, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 847) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465171652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171652 none O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 36, 36, 36, 36, 12, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 12, 12, 12, 12, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 848) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001465171652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171652 none O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 40, 40, 40, 40, 13, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 849) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001465171652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171652 none O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 40, 40, 40, 40, 13, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465171652 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 Building ZINC001465171652 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001465171652 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 846) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465171652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171652 none O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 36, 36, 36, 36, 12, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 12, 12, 12, 12, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 847) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465171652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171652 none O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 36, 36, 36, 36, 12, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 12, 12, 12, 12, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 848) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001465171652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171652 none O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 40, 40, 40, 40, 13, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 849) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001465171652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171652 none O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 40, 40, 40, 40, 13, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465171652 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 Building ZINC001465171652 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001465171652 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 846) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465171652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171652 none O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 36, 36, 36, 36, 12, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 12, 12, 12, 12, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 847) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465171652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171652 none O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 36, 36, 36, 36, 12, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 12, 12, 12, 12, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 848) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171652.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001465171652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171652 none O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 40, 40, 40, 40, 13, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 849) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171652.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001465171652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171652 none O=C(N[C@@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 40, 40, 40, 40, 13, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465171652 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171652 Building ZINC001465171653 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001465171653 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/850 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465171653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171653 none O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 41, 41, 41, 41, 13, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/851 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/851' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465171653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171653 none O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 41, 41, 41, 41, 13, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/852 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/852' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171653.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001465171653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171653 none O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 37, 37, 37, 37, 11, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 4, 11, 11, 11, 11, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/853 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/853' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171653.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001465171653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171653 none O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 37, 37, 37, 37, 11, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 4, 11, 11, 11, 11, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465171653 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 Building ZINC001465171653 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001465171653 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 850) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465171653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171653 none O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 41, 41, 41, 41, 13, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 851) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465171653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171653 none O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 41, 41, 41, 41, 13, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 852) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171653.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001465171653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171653 none O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 37, 37, 37, 37, 11, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 4, 11, 11, 11, 11, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 853) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171653.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001465171653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171653 none O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 37, 37, 37, 37, 11, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 4, 11, 11, 11, 11, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465171653 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 Building ZINC001465171653 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001465171653 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 850) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465171653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171653 none O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 41, 41, 41, 41, 13, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 851) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465171653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171653 none O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 41, 41, 41, 41, 13, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 852) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171653.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001465171653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171653 none O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 37, 37, 37, 37, 11, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 4, 11, 11, 11, 11, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 853) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171653.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001465171653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171653 none O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 37, 37, 37, 37, 11, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 4, 11, 11, 11, 11, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465171653 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 Building ZINC001465171653 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001465171653 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 850) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465171653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171653 none O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 41, 41, 41, 41, 13, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 851) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465171653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171653 none O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 41, 41, 41, 41, 13, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 5, 5, 5, 5, 13, 13, 13, 13, 5, 5, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 852) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171653.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001465171653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171653 none O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 37, 37, 37, 37, 11, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 4, 11, 11, 11, 11, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 853) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001465171653.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001465171653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465171653 none O=C(N[C@H]1CCN(c2cccc(OC(F)(F)F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 37, 37, 37, 37, 11, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 4, 4, 4, 11, 11, 11, 11, 4, 4, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 33, 20, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465171653 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465171653 Building ZINC001465303599 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465303599 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/854 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001465303599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465303599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465303599 none CC(C)(C)OC(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['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', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', '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, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 34, 19, 34, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 38, 38, 38, 38, 38, 38, 38, 38, 38, 19, 10, 10, 10, 10, 2, 5, 5, 10, 10, 10, 10] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/855 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001465303599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465303599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465303599 none CC(C)(C)OC(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['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', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', '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, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 35, 20, 35, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 20, 10, 10, 10, 10, 2, 6, 6, 10, 10, 10, 10] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465303599 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599 Building ZINC001465303599 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465303599 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 854) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001465303599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465303599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465303599 none CC(C)(C)OC(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['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', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', '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, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 34, 19, 34, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 38, 38, 38, 38, 38, 38, 38, 38, 38, 19, 10, 10, 10, 10, 2, 5, 5, 10, 10, 10, 10] 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 855) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1) `ZINC001465303599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465303599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465303599 none CC(C)(C)OC(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1 NO_LONG_NAME dock atom types: ['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', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', '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, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 35, 20, 35, 10, 10, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 37, 37, 37, 37, 37, 37, 37, 37, 37, 20, 10, 10, 10, 10, 2, 6, 6, 10, 10, 10, 10] 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465303599 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465303599 Building ZINC001465317119 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465317119 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/856 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1OCc1cccnc1) `ZINC001465317119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465317119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001465317119 none COc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1OCc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 15, 21, 43, 43, 43, 43, 43, 10, 10, 10, 9, 5, 5, 1, 2, 2, 2, 2, 9, 9, 21, 21, 43, 43, 43, 43] 50 rigid atoms, others: [11, 5, 6, 39, 8, 9, 10, 7] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/857 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1OCc1cccnc1) `ZINC001465317119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465317119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001465317119 none COc1cc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1OCc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 15, 21, 43, 43, 43, 43, 43, 10, 10, 10, 9, 5, 5, 1, 2, 2, 2, 2, 9, 9, 21, 21, 43, 43, 43, 43] 50 rigid atoms, others: [11, 5, 6, 39, 8, 9, 10, 7] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465317119 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119 Building ZINC001465317119 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465317119 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 856) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1OCc1cccnc1) `ZINC001465317119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465317119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001465317119 none COc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1OCc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 15, 21, 43, 43, 43, 43, 43, 10, 10, 10, 9, 5, 5, 1, 2, 2, 2, 2, 9, 9, 21, 21, 43, 43, 43, 43] 50 rigid atoms, others: [11, 5, 6, 39, 8, 9, 10, 7] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 857) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1cc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1OCc1cccnc1) `ZINC001465317119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465317119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001465317119 none COc1cc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)ccc1OCc1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 15, 21, 43, 43, 43, 43, 43, 10, 10, 10, 9, 5, 5, 1, 2, 2, 2, 2, 9, 9, 21, 21, 43, 43, 43, 43] 50 rigid atoms, others: [11, 5, 6, 39, 8, 9, 10, 7] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465317119 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465317119 Building ZINC001465556903 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465556903 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/858 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc2ccccc2c1CN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)CC)CC1) `ZINC001465556903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465556903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001465556903 none CCOC(=O)c1sc2ccccc2c1CN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)CC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 10, 5, 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, 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, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 18, 12, 12, 12, 12, 12, 12, 12, 12, 8, 4, 4, 4, 4, 3, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 4, 18, 18, 18, 18, 18, 12, 12, 12, 12, 8, 8, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/859 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc2ccccc2c1CN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)CC)CC1) `ZINC001465556903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465556903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001465556903 none CCOC(=O)c1sc2ccccc2c1CN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)CC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 10, 5, 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, 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, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 11, 18, 11, 11, 11, 11, 11, 11, 11, 11, 7, 4, 4, 4, 4, 4, 1, 3, 1, 1, 1, 3, 3, 3, 3, 4, 4, 18, 18, 18, 18, 18, 11, 11, 11, 11, 7, 7, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465556903 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903 Building ZINC001465556903 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465556903 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 858) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1sc2ccccc2c1CN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)CC)CC1) `ZINC001465556903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465556903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001465556903 none CCOC(=O)c1sc2ccccc2c1CN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)CC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 10, 5, 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, 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, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 18, 12, 12, 12, 12, 12, 12, 12, 12, 8, 4, 4, 4, 4, 3, 1, 2, 1, 1, 1, 3, 3, 3, 3, 4, 4, 18, 18, 18, 18, 18, 12, 12, 12, 12, 8, 8, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 859) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1sc2ccccc2c1CN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)CC)CC1) `ZINC001465556903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465556903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001465556903 none CCOC(=O)c1sc2ccccc2c1CN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)CC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 1, 5, 10, 5, 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, 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, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 11, 18, 11, 11, 11, 11, 11, 11, 11, 11, 7, 4, 4, 4, 4, 4, 1, 3, 1, 1, 1, 3, 3, 3, 3, 4, 4, 18, 18, 18, 18, 18, 11, 11, 11, 11, 7, 7, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465556903 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465556903 Building ZINC001465682492 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465682492 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/860 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCc1ccccc1)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001465682492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465682492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465682492 none O=C(CCc1ccccc1)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', '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', 'C.3', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 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] dock color type numbers: [6, 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: [27, 17, 27, 49, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 12, 1, 15, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 17, 17, 49, 49, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 2, 1, 2, 17, 17, 17, 17] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/861 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCc1ccccc1)N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001465682492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465682492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465682492 none O=C(CCc1ccccc1)N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', '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', 'C.3', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 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] dock color type numbers: [6, 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: [27, 16, 27, 48, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 11, 1, 14, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 16, 16, 48, 48, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 2, 1, 2, 16, 16, 16, 16] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465682492 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492 Building ZINC001465682492 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465682492 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 860) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(CCc1ccccc1)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001465682492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465682492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465682492 none O=C(CCc1ccccc1)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', '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', 'C.3', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 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] dock color type numbers: [6, 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: [27, 17, 27, 49, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 12, 1, 15, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 17, 17, 49, 49, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 2, 1, 2, 17, 17, 17, 17] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 861) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(CCc1ccccc1)N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001465682492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465682492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001465682492 none O=C(CCc1ccccc1)N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', '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', 'C.3', 'H', 'H', '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, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 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] dock color type numbers: [6, 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: [27, 16, 27, 48, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 11, 1, 14, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 16, 16, 48, 48, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 2, 1, 2, 16, 16, 16, 16] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 179 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465682492 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465682492 Building ZINC001465753402 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465753402 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/862 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Cc1cccc(F)c1)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001465753402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465753402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465753402 none O=C(Cc1cccc(F)c1)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 15, 30, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 8, 1, 9, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 10, 10, 30, 30, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 2, 1, 2, 10, 10, 10, 10] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/863 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Cc1cccc(F)c1)N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001465753402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465753402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465753402 none O=C(Cc1cccc(F)c1)N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 12, 28, 49, 49, 49, 49, 49, 49, 9, 9, 9, 9, 6, 2, 7, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 28, 28, 49, 49, 49, 49, 9, 9, 9, 9, 9, 9, 3, 1, 3, 9, 9, 9, 9] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 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]) total number of confs: 154 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465753402 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402 Building ZINC001465753402 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001465753402 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 862) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Cc1cccc(F)c1)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001465753402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001465753402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465753402 none O=C(Cc1cccc(F)c1)N1CCCN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 15, 30, 50, 50, 50, 50, 50, 50, 10, 10, 10, 10, 8, 1, 9, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 10, 10, 30, 30, 50, 50, 50, 50, 10, 10, 10, 10, 10, 10, 2, 1, 2, 10, 10, 10, 10] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 155 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 863) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Cc1cccc(F)c1)N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1) `ZINC001465753402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001465753402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001465753402 none O=C(Cc1cccc(F)c1)N1CCCN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 12, 28, 49, 49, 49, 49, 49, 49, 9, 9, 9, 9, 6, 2, 7, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 9, 9, 28, 28, 49, 49, 49, 49, 9, 9, 9, 9, 9, 9, 3, 1, 3, 9, 9, 9, 9] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 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]) total number of confs: 154 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001465753402 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001465753402 Building ZINC001466790585 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466790585 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/864 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccc1)C[C@@H](O)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001466790585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466790585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001466790585 none O=C(N(Cc1ccccc1)C[C@@H](O)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 15, 20, 20, 20, 20, 20, 6, 13, 18, 18, 18, 18, 18, 18, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 20, 20, 20, 20, 20, 13, 13, 54, 4, 4] 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]) total number of confs: 187 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/865 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccc1)C[C@@H](O)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001466790585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466790585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001466790585 none O=C(N(Cc1ccccc1)C[C@@H](O)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 21, 25, 25, 22, 25, 25, 8, 14, 19, 19, 19, 19, 19, 19, 1, 1, 1, 4, 4, 4, 4, 4, 21, 21, 25, 25, 25, 25, 25, 14, 14, 57, 4, 4] 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]) total number of confs: 216 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001466790585 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585 Building ZINC001466790585 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466790585 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 864) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N(Cc1ccccc1)C[C@@H](O)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001466790585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466790585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001466790585 none O=C(N(Cc1ccccc1)C[C@@H](O)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 15, 20, 20, 20, 20, 20, 6, 13, 18, 18, 18, 18, 18, 18, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15, 20, 20, 20, 20, 20, 13, 13, 54, 4, 4] 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]) total number of confs: 187 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 865) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N(Cc1ccccc1)C[C@@H](O)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001466790585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466790585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001466790585 none O=C(N(Cc1ccccc1)C[C@@H](O)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 21, 25, 25, 22, 25, 25, 8, 14, 19, 19, 19, 19, 19, 19, 1, 1, 1, 4, 4, 4, 4, 4, 21, 21, 25, 25, 25, 25, 25, 14, 14, 57, 4, 4] 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]) total number of confs: 216 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001466790585 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790585 Building ZINC001466790586 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466790586 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/866 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccc1)C[C@H](O)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001466790586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466790586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001466790586 none O=C(N(Cc1ccccc1)C[C@H](O)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 21, 24, 24, 23, 24, 24, 7, 13, 21, 21, 21, 21, 21, 21, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 24, 24, 24, 24, 24, 13, 13, 63, 5, 5] 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]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/867 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccc1)C[C@H](O)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001466790586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466790586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001466790586 none O=C(N(Cc1ccccc1)C[C@H](O)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 9, 20, 24, 24, 22, 24, 24, 9, 17, 21, 21, 21, 21, 21, 21, 1, 1, 1, 4, 4, 4, 4, 4, 20, 20, 24, 24, 24, 24, 24, 17, 17, 63, 4, 4] 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]) total number of confs: 213 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001466790586 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586 Building ZINC001466790586 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466790586 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 866) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N(Cc1ccccc1)C[C@H](O)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001466790586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466790586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001466790586 none O=C(N(Cc1ccccc1)C[C@H](O)C(F)(F)F)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 21, 24, 24, 23, 24, 24, 7, 13, 21, 21, 21, 21, 21, 21, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 24, 24, 24, 24, 24, 13, 13, 63, 5, 5] 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]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 867) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N(Cc1ccccc1)C[C@H](O)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001466790586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466790586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001466790586 none O=C(N(Cc1ccccc1)C[C@H](O)C(F)(F)F)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 12, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 9, 20, 24, 24, 22, 24, 24, 9, 17, 21, 21, 21, 21, 21, 21, 1, 1, 1, 4, 4, 4, 4, 4, 20, 20, 24, 24, 24, 24, 24, 17, 17, 63, 4, 4] 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]) total number of confs: 213 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001466790586 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466790586 Building ZINC001466798237 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466798237 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/868 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2c(ncn2c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001466798237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466798237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001466798237 none O=C(N1CCc2c(ncn2c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 19, 19, 19, 19, 19, 19, 19, 19, 30, 30, 30, 30, 30, 30, 19, 1, 1, 1, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 30, 30, 30, 30, 19, 19, 5, 5] 50 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/869 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2c(ncn2c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001466798237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466798237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001466798237 none O=C(N1CCc2c(ncn2c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 10, 19, 19, 19, 19, 19, 19, 19, 19, 30, 30, 30, 30, 30, 30, 19, 1, 1, 1, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 30, 30, 30, 30, 19, 19, 5, 5] 50 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001466798237 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237 Building ZINC001466798237 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466798237 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 868) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCc2c(ncn2c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001466798237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466798237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001466798237 none O=C(N1CCc2c(ncn2c2ccc(F)cc2)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 19, 19, 19, 19, 19, 19, 19, 19, 30, 30, 30, 30, 30, 30, 19, 1, 1, 1, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 30, 30, 30, 30, 19, 19, 5, 5] 50 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 869) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCc2c(ncn2c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001466798237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466798237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001466798237 none O=C(N1CCc2c(ncn2c2ccc(F)cc2)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 8, 1, 8, 1, 1, 1, 1, 15, 1, 1, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 10, 19, 19, 19, 19, 19, 19, 19, 19, 30, 30, 30, 30, 30, 30, 19, 1, 1, 1, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 30, 30, 30, 30, 19, 19, 5, 5] 50 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001466798237 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466798237 Building ZINC001466875064 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466875064 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/870 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](CO)Cc1ccccc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001466875064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466875064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001466875064 none O=C(NC[C@H](CO)Cc1ccccc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 13, 34, 31, 40, 34, 47, 50, 50, 47, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 39, 39, 120, 47, 47, 50, 50, 50, 50, 2, 1, 2] 150 rigid atoms, others: [1, 16, 17, 18] 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]) total number of confs: 391 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/871 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](CO)Cc1ccccc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001466875064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466875064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001466875064 none O=C(NC[C@H](CO)Cc1ccccc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 13, 29, 25, 34, 28, 42, 50, 50, 42, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 34, 33, 102, 42, 42, 50, 50, 50, 50, 2, 1, 2] 150 rigid atoms, others: [1, 16, 17, 18] 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]) total number of confs: 396 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001466875064 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064 Building ZINC001466875064 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466875064 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 870) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@H](CO)Cc1ccccc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001466875064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466875064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001466875064 none O=C(NC[C@H](CO)Cc1ccccc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 13, 34, 31, 40, 34, 47, 50, 50, 47, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 39, 39, 120, 47, 47, 50, 50, 50, 50, 2, 1, 2] 150 rigid atoms, others: [1, 16, 17, 18] 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]) total number of confs: 391 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 871) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@H](CO)Cc1ccccc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001466875064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466875064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001466875064 none O=C(NC[C@H](CO)Cc1ccccc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 13, 29, 25, 34, 28, 42, 50, 50, 42, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 34, 33, 102, 42, 42, 50, 50, 50, 50, 2, 1, 2] 150 rigid atoms, others: [1, 16, 17, 18] 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]) total number of confs: 396 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001466875064 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875064 Building ZINC001466875070 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466875070 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/872 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](CO)Cc1ccccc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001466875070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466875070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001466875070 none O=C(NC[C@@H](CO)Cc1ccccc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 31, 27, 35, 29, 42, 50, 50, 42, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 12, 12, 34, 35, 105, 42, 42, 50, 50, 50, 50, 2, 1, 2] 150 rigid atoms, others: [1, 16, 17, 18] 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]) total number of confs: 400 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/873 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](CO)Cc1ccccc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001466875070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466875070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001466875070 none O=C(NC[C@@H](CO)Cc1ccccc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 13, 35, 32, 40, 35, 47, 50, 50, 47, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 39, 39, 120, 47, 47, 50, 50, 50, 50, 2, 1, 2] 150 rigid atoms, others: [1, 16, 17, 18] 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]) total number of confs: 388 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001466875070 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070 Building ZINC001466875070 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001466875070 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 872) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@@H](CO)Cc1ccccc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001466875070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001466875070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001466875070 none O=C(NC[C@@H](CO)Cc1ccccc1Br)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 12, 31, 27, 35, 29, 42, 50, 50, 42, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 12, 12, 34, 35, 105, 42, 42, 50, 50, 50, 50, 2, 1, 2] 150 rigid atoms, others: [1, 16, 17, 18] 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]) total number of confs: 400 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 873) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@@H](CO)Cc1ccccc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001466875070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001466875070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001466875070 none O=C(NC[C@@H](CO)Cc1ccccc1Br)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 5, 12, 5, 1, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 13, 35, 32, 40, 35, 47, 50, 50, 47, 50, 50, 50, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 39, 39, 120, 47, 47, 50, 50, 50, 50, 2, 1, 2] 150 rigid atoms, others: [1, 16, 17, 18] 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]) total number of confs: 388 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001466875070 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001466875070 Building ZINC001467860509 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467860509 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/874 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCOC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001467860509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467860509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001467860509 none CCN(CC)CCOC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 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, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 18, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 18, 18, 18, 18, 7, 7, 7, 3, 3, 3, 3, 3, 7] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/875 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CCOC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001467860509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467860509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001467860509 none CCN(CC)CCOC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 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, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 27, 27, 16, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 16, 16, 16, 16, 6, 6, 6, 2, 2, 2, 2, 2, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001467860509 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509 Building ZINC001467860509 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467860509 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 874) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN(CC)CCOC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001467860509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467860509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001467860509 none CCN(CC)CCOC(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 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, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 18, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 18, 18, 18, 18, 7, 7, 7, 3, 3, 3, 3, 3, 7] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 875) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCN(CC)CCOC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1) `ZINC001467860509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467860509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001467860509 none CCN(CC)CCOC(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', '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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 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, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 27, 27, 16, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 16, 16, 16, 16, 6, 6, 6, 2, 2, 2, 2, 2, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001467860509 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467860509 Building ZINC001467928488 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467928488 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/876 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCc1ccccc1)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001467928488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467928488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001467928488 none O=C(CCCc1ccccc1)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 16, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1] 50 rigid atoms, others: [19, 33, 18, 17, 48, 11, 12, 13, 14, 15, 16, 49, 50, 51, 20, 46, 22, 56, 57, 47, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54, 55]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/877 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/877' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCc1ccccc1)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001467928488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467928488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001467928488 none O=C(CCCc1ccccc1)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 14, 20, 30, 30, 30, 30, 30, 30, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 25, 25, 30, 30, 30, 30, 30, 30, 30, 3, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001467928488 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488 Building ZINC001467928488 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467928488 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 876) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(CCCc1ccccc1)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001467928488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467928488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001467928488 none O=C(CCCc1ccccc1)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 16, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1] 50 rigid atoms, others: [19, 33, 18, 17, 48, 11, 12, 13, 14, 15, 16, 49, 50, 51, 20, 46, 22, 56, 57, 47, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 52, 53, 54, 55]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 877) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(CCCc1ccccc1)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001467928488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467928488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001467928488 none O=C(CCCc1ccccc1)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 14, 20, 30, 30, 30, 30, 30, 30, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 14, 14, 25, 25, 30, 30, 30, 30, 30, 30, 30, 3, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001467928488 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928488 Building ZINC001467928490 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467928490 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/878 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCc1ccccc1)N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001467928490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467928490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001467928490 none O=C(CCCc1ccccc1)N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 15, 21, 30, 30, 30, 30, 30, 30, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 15, 15, 26, 26, 30, 30, 30, 30, 30, 30, 30, 3, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 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/6899/xaj-8058088.10/working/building/ZINC001467928490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/879 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCc1ccccc1)N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001467928490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467928490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001467928490 none O=C(CCCc1ccccc1)N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 13, 18, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001467928490 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490 Building ZINC001467928490 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001467928490 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 878) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(CCCc1ccccc1)N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001467928490.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001467928490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001467928490 none O=C(CCCc1ccccc1)N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 15, 21, 30, 30, 30, 30, 30, 30, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 15, 15, 26, 26, 30, 30, 30, 30, 30, 30, 30, 3, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 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/6899/xaj-8058088.10/working/building/ZINC001467928490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 879) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(CCCc1ccccc1)N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1) `ZINC001467928490.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001467928490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001467928490 none O=C(CCCc1ccccc1)N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 13, 18, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 2, 2] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001467928490 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001467928490 Building ZINC001468091040 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468091040 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/880 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(Br)cccc1C[C@@H](CO)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001468091040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468091040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468091040 none Cc1c(Br)cccc1C[C@@H](CO)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 26, 18, 11, 18, 18, 21, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 37, 37, 37, 37, 37, 37, 26, 26, 21, 21, 63, 11, 11, 2, 6, 6] 150 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]) total number of confs: 225 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/881 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/881' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(Br)cccc1C[C@@H](CO)CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001468091040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468091040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468091040 none Cc1c(Br)cccc1C[C@@H](CO)CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 29, 21, 12, 21, 21, 23, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 38, 38, 38, 38, 38, 38, 29, 29, 23, 23, 69, 12, 12, 3, 6, 6] 150 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]) total number of confs: 232 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468091040 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040 Building ZINC001468091040 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468091040 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 880) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1c(Br)cccc1C[C@@H](CO)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001468091040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468091040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468091040 none Cc1c(Br)cccc1C[C@@H](CO)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 26, 18, 11, 18, 18, 21, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 37, 37, 37, 37, 37, 37, 26, 26, 21, 21, 63, 11, 11, 2, 6, 6] 150 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]) total number of confs: 225 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 881) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1c(Br)cccc1C[C@@H](CO)CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001468091040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468091040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468091040 none Cc1c(Br)cccc1C[C@@H](CO)CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 29, 21, 12, 21, 21, 23, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 38, 38, 38, 38, 38, 38, 29, 29, 23, 23, 69, 12, 12, 3, 6, 6] 150 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]) total number of confs: 232 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468091040 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091040 Building ZINC001468091044 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468091044 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/882 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(Br)cccc1C[C@H](CO)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001468091044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468091044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468091044 none Cc1c(Br)cccc1C[C@H](CO)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 29, 21, 12, 21, 21, 23, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 38, 38, 38, 38, 38, 38, 29, 29, 23, 23, 69, 12, 12, 3, 6, 6] 150 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]) total number of confs: 232 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/883 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(Br)cccc1C[C@H](CO)CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001468091044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468091044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468091044 none Cc1c(Br)cccc1C[C@H](CO)CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 26, 18, 11, 18, 18, 21, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 37, 37, 37, 37, 37, 37, 26, 26, 21, 21, 63, 11, 11, 2, 6, 6] 150 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]) total number of confs: 225 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468091044 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044 Building ZINC001468091044 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468091044 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 882) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1c(Br)cccc1C[C@H](CO)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001468091044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468091044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468091044 none Cc1c(Br)cccc1C[C@H](CO)CNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 29, 21, 12, 21, 21, 23, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 38, 38, 38, 38, 38, 38, 29, 29, 23, 23, 69, 12, 12, 3, 6, 6] 150 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]) total number of confs: 232 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 883) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1c(Br)cccc1C[C@H](CO)CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC001468091044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468091044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468091044 none Cc1c(Br)cccc1C[C@H](CO)CNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 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, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 26, 18, 11, 18, 18, 21, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 37, 37, 37, 37, 37, 37, 26, 26, 21, 21, 63, 11, 11, 2, 6, 6] 150 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]) total number of confs: 225 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468091044 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468091044 Building ZINC001468140511 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468140511 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/884 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@@H](CO)CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1Br) `ZINC001468140511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468140511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468140511 none Cc1ccc(C[C@@H](CO)CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.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.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 25, 21, 13, 21, 21, 22, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 25, 25, 22, 22, 66, 13, 13, 2, 6, 6, 38] 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]) total number of confs: 220 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/885 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@@H](CO)CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1Br) `ZINC001468140511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468140511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468140511 none Cc1ccc(C[C@@H](CO)CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.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.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 25, 22, 13, 22, 22, 23, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 41, 41, 41, 41, 41, 41, 41, 41, 25, 25, 23, 23, 69, 13, 13, 4, 6, 6, 41] 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]) total number of confs: 224 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468140511 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511 Building ZINC001468140511 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468140511 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 884) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(C[C@@H](CO)CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1Br) `ZINC001468140511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468140511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468140511 none Cc1ccc(C[C@@H](CO)CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.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.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 25, 21, 13, 21, 21, 22, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 25, 25, 22, 22, 66, 13, 13, 2, 6, 6, 38] 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]) total number of confs: 220 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 885) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(C[C@@H](CO)CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1Br) `ZINC001468140511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468140511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468140511 none Cc1ccc(C[C@@H](CO)CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.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.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 25, 22, 13, 22, 22, 23, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 41, 41, 41, 41, 41, 41, 41, 41, 25, 25, 23, 23, 69, 13, 13, 4, 6, 6, 41] 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]) total number of confs: 224 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468140511 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140511 Building ZINC001468140512 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468140512 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/886 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@H](CO)CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1Br) `ZINC001468140512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468140512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468140512 none Cc1ccc(C[C@H](CO)CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.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.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 25, 22, 13, 22, 22, 23, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 41, 41, 41, 41, 41, 41, 41, 41, 25, 25, 23, 23, 69, 13, 13, 4, 6, 6, 41] 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]) total number of confs: 224 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/887 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C[C@H](CO)CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1Br) `ZINC001468140512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468140512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468140512 none Cc1ccc(C[C@H](CO)CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.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.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 25, 21, 13, 21, 21, 22, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 25, 25, 22, 22, 66, 13, 13, 2, 6, 6, 38] 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]) total number of confs: 220 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468140512 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512 Building ZINC001468140512 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468140512 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 886) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(C[C@H](CO)CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1Br) `ZINC001468140512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468140512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468140512 none Cc1ccc(C[C@H](CO)CNC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.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.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 25, 22, 13, 22, 22, 23, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 41, 41, 41, 41, 41, 41, 41, 41, 25, 25, 23, 23, 69, 13, 13, 4, 6, 6, 41] 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]) total number of confs: 224 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 887) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(C[C@H](CO)CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1Br) `ZINC001468140512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468140512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001468140512 none Cc1ccc(C[C@H](CO)CNC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.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.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 25, 21, 13, 21, 21, 22, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 25, 25, 22, 22, 66, 13, 13, 2, 6, 6, 38] 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]) total number of confs: 220 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468140512 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468140512 Building ZINC001468163384 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468163384 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/888 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CCO[C@H]1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001468163384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468163384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001468163384 none CC(C)(C)OC(=O)N[C@@H]1CCO[C@H]1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 38, 26, 38, 14, 14, 14, 14, 14, 14, 4, 14, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 40, 26, 14, 14, 14, 14, 8, 4, 4, 4, 4, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/889 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CCO[C@H]1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001468163384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468163384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001468163384 none CC(C)(C)OC(=O)N[C@@H]1CCO[C@H]1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 33, 43, 20, 20, 20, 20, 20, 20, 5, 20, 5, 5, 5, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 33, 20, 20, 20, 20, 9, 5, 5, 5, 5, 2, 2, 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, 50, 51, 52, 53, 54, 55]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468163384 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384 Building ZINC001468163384 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468163384 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 888) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/888: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CCO[C@H]1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001468163384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468163384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001468163384 none CC(C)(C)OC(=O)N[C@@H]1CCO[C@H]1C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 38, 26, 38, 14, 14, 14, 14, 14, 14, 4, 14, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 40, 26, 14, 14, 14, 14, 8, 4, 4, 4, 4, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 889) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/889: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CCO[C@H]1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC001468163384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468163384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001468163384 none CC(C)(C)OC(=O)N[C@@H]1CCO[C@H]1C1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 33, 43, 20, 20, 20, 20, 20, 20, 5, 20, 5, 5, 5, 2, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 33, 20, 20, 20, 20, 9, 5, 5, 5, 5, 2, 2, 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, 50, 51, 52, 53, 54, 55]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468163384 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468163384 Building ZINC001468185337 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001468185337 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/890 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468185337.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468185337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468185337 none O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 13, 15, 15, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 35, 35, 35, 15, 15, 15, 15, 2, 2] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/891 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468185337.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468185337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468185337 none O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 13, 15, 15, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 35, 35, 35, 15, 15, 15, 15, 2, 2] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/892 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/892' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468185337.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001468185337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468185337 none O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 13, 15, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 37, 37, 37, 15, 15, 15, 15, 2, 2] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/893 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/893' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468185337.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001468185337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468185337 none O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 13, 15, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 37, 37, 37, 15, 15, 15, 15, 2, 2] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468185337 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 Building ZINC001468185337 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001468185337 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 890) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468185337.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468185337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468185337 none O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 13, 15, 15, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 35, 35, 35, 15, 15, 15, 15, 2, 2] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 891) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468185337.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468185337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468185337 none O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 13, 15, 15, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 35, 35, 35, 15, 15, 15, 15, 2, 2] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 892) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N1CCCN(c2cccc(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468185337.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001468185337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468185337 none O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 13, 15, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 37, 37, 37, 15, 15, 15, 15, 2, 2] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 893) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N1CCCN(c2cccc(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468185337.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001468185337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468185337 none O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 13, 15, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 37, 37, 37, 15, 15, 15, 15, 2, 2] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468185337 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 Building ZINC001468185337 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001468185337 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 890) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468185337.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468185337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468185337 none O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 13, 15, 15, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 35, 35, 35, 15, 15, 15, 15, 2, 2] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 891) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468185337.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468185337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468185337 none O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 13, 15, 15, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 35, 35, 35, 15, 15, 15, 15, 2, 2] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 892) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N1CCCN(c2cccc(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468185337.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001468185337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468185337 none O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 13, 15, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 37, 37, 37, 15, 15, 15, 15, 2, 2] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 893) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N1CCCN(c2cccc(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468185337.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001468185337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468185337 none O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 13, 15, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 37, 37, 37, 15, 15, 15, 15, 2, 2] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468185337 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 Building ZINC001468185337 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001468185337 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 890) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468185337.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468185337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468185337 none O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 13, 15, 15, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 35, 35, 35, 15, 15, 15, 15, 2, 2] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 891) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468185337.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468185337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468185337 none O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 13, 15, 15, 15, 15, 15, 35, 35, 35, 35, 35, 35, 35, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 35, 35, 35, 15, 15, 15, 15, 2, 2] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 892) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N1CCCN(c2cccc(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468185337.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001468185337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468185337 none O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 13, 15, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 37, 37, 37, 15, 15, 15, 15, 2, 2] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 893) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N1CCCN(c2cccc(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468185337.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001468185337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001468185337 none O=C(N1CCCN(c2cccc(F)c2F)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 15, 1, 15, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 13, 15, 15, 15, 15, 15, 37, 37, 37, 37, 37, 37, 37, 15, 15, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 37, 37, 37, 15, 15, 15, 15, 2, 2] 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468185337 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468185337 Building ZINC001468198265 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468198265 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/894 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(F)(F)F)n2[C@H](C)CCO) `ZINC001468198265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468198265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001468198265 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(F)(F)F)n2[C@H](C)CCO 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', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 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: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 43, 48, 3, 3, 3, 3, 3, 3, 3, 5, 21, 21, 21, 21, 21, 21, 43, 43, 48, 48, 144] 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: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/895 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(F)(F)F)n2[C@H](C)CCO) `ZINC001468198265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468198265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001468198265 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(F)(F)F)n2[C@H](C)CCO 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', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 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: [4, 4, 4, 4, 3, 4, 4, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 42, 48, 4, 4, 4, 4, 4, 4, 4, 6, 22, 22, 22, 22, 22, 22, 42, 42, 48, 48, 144] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 321 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468198265 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265 Building ZINC001468198265 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468198265 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 894) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(F)(F)F)n2[C@H](C)CCO) `ZINC001468198265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468198265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001468198265 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(F)(F)F)n2[C@H](C)CCO 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', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 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: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 43, 48, 3, 3, 3, 3, 3, 3, 3, 5, 21, 21, 21, 21, 21, 21, 43, 43, 48, 48, 144] 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: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 895) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(F)(F)F)n2[C@H](C)CCO) `ZINC001468198265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468198265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001468198265 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(F)(F)F)n2[C@H](C)CCO 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', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 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: [4, 4, 4, 4, 3, 4, 4, 1, 1, 1, 1, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 42, 48, 4, 4, 4, 4, 4, 4, 4, 6, 22, 22, 22, 22, 22, 22, 42, 42, 48, 48, 144] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 321 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468198265 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198265 Building ZINC001468198268 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468198268 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/896 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(F)(F)F)n2[C@@H](C)CCO) `ZINC001468198268.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468198268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001468198268 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(F)(F)F)n2[C@@H](C)CCO 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', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 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: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 42, 48, 3, 3, 3, 3, 3, 3, 3, 5, 22, 22, 22, 22, 22, 22, 42, 42, 48, 48, 144] 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: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/897 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(F)(F)F)n2[C@@H](C)CCO) `ZINC001468198268.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468198268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001468198268 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(F)(F)F)n2[C@@H](C)CCO 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', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 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: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 42, 47, 3, 3, 3, 3, 3, 3, 3, 5, 21, 21, 21, 21, 21, 21, 42, 42, 47, 47, 141] 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: 316 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468198268 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268 Building ZINC001468198268 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468198268 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 896) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(F)(F)F)n2[C@@H](C)CCO) `ZINC001468198268.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468198268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001468198268 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(F)(F)F)n2[C@@H](C)CCO 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', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 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: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 42, 48, 3, 3, 3, 3, 3, 3, 3, 5, 22, 22, 22, 22, 22, 22, 42, 42, 48, 48, 144] 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: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 897) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(F)(F)F)n2[C@@H](C)CCO) `ZINC001468198268.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468198268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001468198268 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)nc(C(F)(F)F)n2[C@@H](C)CCO 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', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] 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, 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: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 42, 47, 3, 3, 3, 3, 3, 3, 3, 5, 21, 21, 21, 21, 21, 21, 42, 42, 47, 47, 141] 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: 316 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468198268 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468198268 Building ZINC001468561160 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468561160 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/898 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(Oc2cncc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468561160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468561160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001468561160 none O=C(N1CCC(Oc2cncc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.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, 5, 12, 1, 1, 8, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 7, 7, 3, 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] 0 hydrogens need 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, 4, 4, 4, 4, 17, 38, 38, 38, 38, 38, 38, 4, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 38, 38, 38, 4, 4, 4, 4, 2, 2] 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/899 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(Oc2cncc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468561160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468561160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001468561160 none O=C(N1CCC(Oc2cncc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.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, 5, 12, 1, 1, 8, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 7, 7, 3, 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] 0 hydrogens need 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, 4, 4, 4, 4, 15, 35, 35, 35, 35, 35, 35, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468561160 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160 Building ZINC001468561160 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468561160 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 898) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCC(Oc2cncc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468561160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468561160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001468561160 none O=C(N1CCC(Oc2cncc(Cl)c2)CC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.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, 5, 12, 1, 1, 8, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 7, 7, 3, 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] 0 hydrogens need 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, 4, 4, 4, 4, 17, 38, 38, 38, 38, 38, 38, 4, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 38, 38, 38, 4, 4, 4, 4, 2, 2] 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 899) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCC(Oc2cncc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468561160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468561160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001468561160 none O=C(N1CCC(Oc2cncc(Cl)c2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.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, 5, 12, 1, 1, 8, 1, 1, 16, 1, 5, 5, 5, 12, 1, 1, 1, 1, 17, 14, 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, 7, 7, 3, 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] 0 hydrogens need 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, 4, 4, 4, 4, 15, 35, 35, 35, 35, 35, 35, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 4, 4, 4, 4, 4, 4] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468561160 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468561160 Building ZINC001468587453 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468587453 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/900 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/900' -> `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](C)CCCCNC(=O)OC(C)(C)C) `ZINC001468587453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468587453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001468587453 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCCCNC(=O)OC(C)(C)C 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', 'C.3', 'C.3', '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', '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, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 3, 3, 3, 6, 6, 6, 18, 36, 46, 46, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 3, 3, 3, 6, 6, 6, 6, 6, 6, 18, 18, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/901 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/901' -> `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](C)CCCCNC(=O)OC(C)(C)C) `ZINC001468587453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468587453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001468587453 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCCCNC(=O)OC(C)(C)C 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', 'C.3', 'C.3', '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', '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, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 3, 3, 3, 6, 6, 6, 13, 36, 48, 48, 49, 49, 49, 49, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 3, 6, 6, 6, 6, 6, 6, 13, 13, 36, 49, 49, 49, 49, 49, 49, 49, 49, 49] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468587453 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453 Building ZINC001468587453 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468587453 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 900) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCCCNC(=O)OC(C)(C)C) `ZINC001468587453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468587453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001468587453 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCCCNC(=O)OC(C)(C)C 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', 'C.3', 'C.3', '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', '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, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 3, 3, 3, 6, 6, 6, 18, 36, 46, 46, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 3, 3, 3, 6, 6, 6, 6, 6, 6, 18, 18, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 901) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCCCNC(=O)OC(C)(C)C) `ZINC001468587453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468587453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001468587453 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCCCNC(=O)OC(C)(C)C 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', 'C.3', 'C.3', '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', '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, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 3, 3, 3, 6, 6, 6, 13, 36, 48, 48, 49, 49, 49, 49, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 3, 6, 6, 6, 6, 6, 6, 13, 13, 36, 49, 49, 49, 49, 49, 49, 49, 49, 49] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468587453 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587453 Building ZINC001468587455 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468587455 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/902 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/902' -> `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](C)CCCCNC(=O)OC(C)(C)C) `ZINC001468587455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468587455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001468587455 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCCCNC(=O)OC(C)(C)C 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', 'C.3', 'C.3', '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', '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, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 3, 3, 3, 5, 5, 5, 12, 35, 48, 48, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 3, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/903 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/903' -> `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](C)CCCCNC(=O)OC(C)(C)C) `ZINC001468587455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468587455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001468587455 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCCCNC(=O)OC(C)(C)C 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', 'C.3', 'C.3', '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', '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, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 3, 3, 3, 6, 6, 6, 17, 38, 49, 49, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 3, 6, 6, 6, 6, 6, 6, 17, 17, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468587455 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455 Building ZINC001468587455 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468587455 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 902) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCCCNC(=O)OC(C)(C)C) `ZINC001468587455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468587455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001468587455 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCCCNC(=O)OC(C)(C)C 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', 'C.3', 'C.3', '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', '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, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 3, 3, 3, 5, 5, 5, 12, 35, 48, 48, 50, 50, 50, 50, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 3, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 903) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCCCNC(=O)OC(C)(C)C) `ZINC001468587455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468587455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001468587455 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCCCNC(=O)OC(C)(C)C 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', 'C.3', 'C.3', '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', '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, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 2, 3, 3, 3, 6, 6, 6, 17, 38, 49, 49, 50, 50, 50, 50, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 3, 3, 3, 6, 6, 6, 6, 6, 6, 17, 17, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50] 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468587455 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468587455 Building ZINC001468590127 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468590127 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/904 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468590127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468590127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001468590127 none C[C@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [4, 2, 4, 4, 8, 9, 9, 19, 36, 44, 44, 46, 46, 46, 46, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 9, 9, 9, 9, 19, 19, 36, 46, 46, 46, 46, 46, 46, 46, 46, 46, 2, 4, 4] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/905 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468590127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468590127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001468590127 none C[C@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [4, 2, 4, 4, 8, 9, 9, 20, 38, 48, 48, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 9, 9, 9, 9, 20, 20, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 3] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468590127 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127 Building ZINC001468590127 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468590127 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 904) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468590127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468590127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001468590127 none C[C@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [4, 2, 4, 4, 8, 9, 9, 19, 36, 44, 44, 46, 46, 46, 46, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 9, 9, 9, 9, 19, 19, 36, 46, 46, 46, 46, 46, 46, 46, 46, 46, 2, 4, 4] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 905) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: C[C@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468590127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468590127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001468590127 none C[C@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [4, 2, 4, 4, 8, 9, 9, 20, 38, 48, 48, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 8, 8, 9, 9, 9, 9, 20, 20, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 3, 3] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468590127 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590127 Building ZINC001468590128 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468590128 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/906 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468590128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468590128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001468590128 none C[C@@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [4, 2, 4, 4, 8, 9, 9, 20, 38, 48, 48, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 9, 9, 9, 9, 20, 20, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 4] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/907 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468590128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468590128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001468590128 none C[C@@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [4, 2, 4, 4, 7, 8, 8, 18, 35, 43, 43, 46, 46, 46, 46, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 7, 7, 8, 8, 8, 8, 18, 18, 35, 46, 46, 46, 46, 46, 46, 46, 46, 46, 2, 3, 3] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468590128 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128 Building ZINC001468590128 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468590128 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 906) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468590128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468590128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001468590128 none C[C@@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [4, 2, 4, 4, 8, 9, 9, 20, 38, 48, 48, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 9, 9, 9, 9, 20, 20, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 4, 4] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 907) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001468590128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468590128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001468590128 none C[C@@H](CCCCNC(=O)OC(C)(C)C)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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: [4, 2, 4, 4, 7, 8, 8, 18, 35, 43, 43, 46, 46, 46, 46, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 7, 7, 8, 8, 8, 8, 18, 18, 35, 46, 46, 46, 46, 46, 46, 46, 46, 46, 2, 3, 3] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468590128 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468590128 Building ZINC001468660019 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468660019 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/908 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)OC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001468660019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468660019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468660019 none O=C(NC1CCCCC1)OC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 33, 33, 33, 33, 33, 4, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/909 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)OC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001468660019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468660019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468660019 none O=C(NC1CCCCC1)OC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 41, 41, 41, 41, 41, 4, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468660019 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019 Building ZINC001468660019 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468660019 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 908) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC1CCCCC1)OC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001468660019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468660019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468660019 none O=C(NC1CCCCC1)OC[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 33, 33, 33, 33, 33, 4, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 909) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC1CCCCC1)OC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001468660019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468660019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468660019 none O=C(NC1CCCCC1)OC[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 41, 41, 41, 41, 41, 4, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468660019 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660019 Building ZINC001468660021 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468660021 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/910 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)OC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001468660021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468660021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468660021 none O=C(NC1CCCCC1)OC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 40, 40, 40, 40, 40, 4, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/911 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)OC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001468660021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468660021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468660021 none O=C(NC1CCCCC1)OC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 33, 33, 33, 33, 33, 4, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468660021 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021 Building ZINC001468660021 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468660021 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 910) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)OC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001468660021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468660021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468660021 none O=C(NC1CCCCC1)OC[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 40, 40, 40, 40, 40, 4, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 911) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCCCC1)OC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001468660021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468660021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468660021 none O=C(NC1CCCCC1)OC[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 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, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 33, 33, 33, 33, 33, 4, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468660021 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468660021 Building ZINC001468853445 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468853445 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/912 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]2C1) `ZINC001468853445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468853445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468853445 none CC(C)(C)OC(=O)N1C[C@@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 17, 9, 17, 9, 9, 9, 9, 9, 9, 4, 9, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 4, 8, 8, 8, 8, 9, 9, 9, 9] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/913 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]2C1) `ZINC001468853445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468853445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468853445 none CC(C)(C)OC(=O)N1C[C@@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 18, 9, 9, 9, 9, 9, 9, 4, 9, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 9, 9, 4, 7, 7, 7, 7, 9, 9, 9, 9] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468853445 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445 Building ZINC001468853445 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468853445 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 912) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1C[C@@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]2C1) `ZINC001468853445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468853445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468853445 none CC(C)(C)OC(=O)N1C[C@@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 17, 9, 17, 9, 9, 9, 9, 9, 9, 4, 9, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 4, 8, 8, 8, 8, 9, 9, 9, 9] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 913) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1C[C@@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]2C1) `ZINC001468853445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468853445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468853445 none CC(C)(C)OC(=O)N1C[C@@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 18, 9, 9, 9, 9, 9, 9, 4, 9, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 9, 9, 4, 7, 7, 7, 7, 9, 9, 9, 9] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468853445 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853445 Building ZINC001468853446 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468853446 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/914 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]2C1) `ZINC001468853446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468853446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468853446 none CC(C)(C)OC(=O)N1C[C@@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 12, 21, 12, 12, 12, 12, 12, 12, 3, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12, 12, 12, 12, 12, 12, 3, 6, 6, 6, 6, 12, 12, 12, 12] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 79 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/915 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]2C1) `ZINC001468853446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468853446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468853446 none CC(C)(C)OC(=O)N1C[C@@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 13, 22, 13, 13, 13, 13, 13, 13, 3, 13, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 13, 13, 13, 13, 13, 3, 6, 6, 6, 6, 13, 13, 13, 13] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468853446 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446 Building ZINC001468853446 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468853446 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 914) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]2C1) `ZINC001468853446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468853446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468853446 none CC(C)(C)OC(=O)N1C[C@@H]2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 12, 21, 12, 12, 12, 12, 12, 12, 3, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 12, 12, 12, 12, 12, 12, 3, 6, 6, 6, 6, 12, 12, 12, 12] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 79 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 915) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]2C1) `ZINC001468853446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468853446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468853446 none CC(C)(C)OC(=O)N1C[C@@H]2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 13, 22, 13, 13, 13, 13, 13, 13, 3, 13, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 13, 13, 13, 13, 13, 3, 6, 6, 6, 6, 13, 13, 13, 13] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 85 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468853446 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853446 Building ZINC001468853447 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468853447 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/916 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]2C1) `ZINC001468853447.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468853447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468853447 none CC(C)(C)OC(=O)N1C[C@@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 14, 21, 14, 14, 14, 14, 14, 14, 4, 14, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 3, 7, 7, 7, 7, 14, 14, 14, 14] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/917 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]2C1) `ZINC001468853447.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468853447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468853447 none CC(C)(C)OC(=O)N1C[C@@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 22, 14, 14, 14, 14, 14, 14, 5, 14, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 4, 8, 8, 8, 8, 14, 14, 14, 14] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468853447 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447 Building ZINC001468853447 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468853447 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 916) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1C[C@@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]2C1) `ZINC001468853447.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468853447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468853447 none CC(C)(C)OC(=O)N1C[C@@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 14, 21, 14, 14, 14, 14, 14, 14, 4, 14, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 3, 7, 7, 7, 7, 14, 14, 14, 14] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 917) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1C[C@@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]2C1) `ZINC001468853447.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468853447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468853447 none CC(C)(C)OC(=O)N1C[C@@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 22, 14, 14, 14, 14, 14, 14, 5, 14, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 14, 4, 8, 8, 8, 8, 14, 14, 14, 14] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468853447 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853447 Building ZINC001468853448 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468853448 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/918 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]2C1) `ZINC001468853448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468853448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468853448 none CC(C)(C)OC(=O)N1C[C@@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 16, 30, 16, 16, 16, 16, 16, 16, 3, 16, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 16, 3, 6, 6, 6, 6, 16, 16, 16, 16] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/919 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]2C1) `ZINC001468853448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468853448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468853448 none CC(C)(C)OC(=O)N1C[C@@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 17, 29, 17, 17, 17, 17, 17, 17, 4, 17, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 17, 17, 17, 17, 17, 17, 3, 6, 6, 6, 6, 17, 17, 17, 17] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468853448 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448 Building ZINC001468853448 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001468853448 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 918) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1C[C@@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]2C1) `ZINC001468853448.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001468853448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468853448 none CC(C)(C)OC(=O)N1C[C@@H]2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 16, 30, 16, 16, 16, 16, 16, 16, 3, 16, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 16, 3, 6, 6, 6, 6, 16, 16, 16, 16] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 919) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1C[C@@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]2C1) `ZINC001468853448.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001468853448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001468853448 none CC(C)(C)OC(=O)N1C[C@@H]2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 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] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 17, 29, 17, 17, 17, 17, 17, 17, 4, 17, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 17, 17, 17, 17, 17, 17, 3, 6, 6, 6, 6, 17, 17, 17, 17] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001468853448 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001468853448 Building ZINC001469045668 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469045668 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/920 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N(CCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)OCc1ccccc1) `ZINC001469045668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469045668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001469045668 none CC(C)(C)OC(=O)N(CCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 23, 23, 23, 23, 23, 12, 9, 7, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 37, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 9, 9, 9, 9, 6, 6, 1, 1, 1, 2, 1, 1, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [51, 50, 54, 17, 11, 12, 13, 14, 15, 16, 49, 18, 19, 20, 21, 22, 23, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 52, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/921 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N(CCCCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)OCc1ccccc1) `ZINC001469045668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469045668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001469045668 none CC(C)(C)OC(=O)N(CCCCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 22, 22, 22, 22, 22, 22, 11, 9, 8, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 22, 36, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 11, 9, 9, 9, 9, 6, 6, 2, 2, 2, 4, 2, 2, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469045668 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668 Building ZINC001469045668 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469045668 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 920) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N(CCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)OCc1ccccc1) `ZINC001469045668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469045668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001469045668 none CC(C)(C)OC(=O)N(CCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1)OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 23, 23, 23, 23, 23, 12, 9, 7, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 37, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 9, 9, 9, 9, 6, 6, 1, 1, 1, 2, 1, 1, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [51, 50, 54, 17, 11, 12, 13, 14, 15, 16, 49, 18, 19, 20, 21, 22, 23, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 52, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 921) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N(CCCCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)OCc1ccccc1) `ZINC001469045668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469045668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001469045668 none CC(C)(C)OC(=O)N(CCCCNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1)OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 22, 22, 22, 22, 22, 22, 11, 9, 8, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 22, 36, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 11, 9, 9, 9, 9, 6, 6, 2, 2, 2, 4, 2, 2, 50, 50, 50, 50, 50, 50, 50] 100 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469045668 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469045668 Building ZINC001469054813 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469054813 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/922 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1(C)C) `ZINC001469054813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469054813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001469054813 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 31, 31, 18, 9, 18, 9, 9, 9, 5, 2, 6, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 9, 9, 9, 9, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/923 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1(C)C) `ZINC001469054813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469054813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001469054813 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 23, 14, 23, 14, 14, 14, 7, 2, 8, 1, 1, 1, 4, 4, 4, 4, 4, 14, 14, 14, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 14, 14, 14, 14, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469054813 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813 Building ZINC001469054813 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469054813 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 922) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1(C)C) `ZINC001469054813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469054813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001469054813 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 31, 31, 18, 9, 18, 9, 9, 9, 5, 2, 6, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 9, 9, 9, 9, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9] 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]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 923) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1(C)C) `ZINC001469054813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469054813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001469054813 none CC(C)(C)OC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)CC1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 23, 14, 23, 14, 14, 14, 7, 2, 8, 1, 1, 1, 4, 4, 4, 4, 4, 14, 14, 14, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 14, 14, 14, 14, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469054813 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469054813 Building ZINC001469243510 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469243510 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/924 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2nc[nH]c2[C@H]1c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001469243510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469243510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001469243510 none O=C(N1CCc2nc[nH]c2[C@H]1c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 8, 1, 8, 6, 1, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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, 4, 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] 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: [9, 2, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 18, 18, 13, 18, 18, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 13, 13, 13, 13, 13, 18, 18, 18, 18, 6, 6, 6, 6] 20 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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/6899/xaj-8058088.10/working/building/ZINC001469243510 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/925 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2nc[nH]c2[C@H]1c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001469243510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469243510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001469243510 none O=C(N1CCc2nc[nH]c2[C@H]1c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 8, 1, 8, 6, 1, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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, 4, 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 16, 17, 18, 18, 1, 1, 1, 5, 5, 1, 1, 5, 5, 14, 14, 14, 14, 14, 18, 18, 18, 18, 5, 5, 5, 5] 19 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469243510 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510 Building ZINC001469243510 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469243510 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 924) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCc2nc[nH]c2[C@H]1c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001469243510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469243510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001469243510 none O=C(N1CCc2nc[nH]c2[C@H]1c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 8, 1, 8, 6, 1, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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, 4, 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] 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: [9, 2, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 18, 18, 13, 18, 18, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 13, 13, 13, 13, 13, 18, 18, 18, 18, 6, 6, 6, 6] 20 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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/6899/xaj-8058088.10/working/building/ZINC001469243510 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 925) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCc2nc[nH]c2[C@H]1c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001469243510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469243510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001469243510 none O=C(N1CCc2nc[nH]c2[C@H]1c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 8, 1, 8, 6, 1, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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, 4, 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] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 16, 17, 18, 18, 1, 1, 1, 5, 5, 1, 1, 5, 5, 14, 14, 14, 14, 14, 18, 18, 18, 18, 5, 5, 5, 5] 19 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469243510 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243510 Building ZINC001469243511 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469243511 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/926 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2nc[nH]c2[C@@H]1c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001469243511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469243511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001469243511 none O=C(N1CCc2nc[nH]c2[C@@H]1c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 8, 1, 8, 6, 1, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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, 4, 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] 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: [9, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 19, 19, 16, 19, 19, 19, 1, 1, 1, 5, 5, 1, 2, 5, 5, 15, 15, 15, 15, 15, 19, 19, 19, 19, 5, 5, 5, 5] 20 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/927 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2nc[nH]c2[C@@H]1c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001469243511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469243511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001469243511 none O=C(N1CCc2nc[nH]c2[C@@H]1c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 8, 1, 8, 6, 1, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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, 4, 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] 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: [9, 2, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 18, 18, 13, 18, 18, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 13, 13, 13, 13, 13, 18, 18, 18, 18, 6, 6, 6, 6] 20 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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/6899/xaj-8058088.10/working/building/ZINC001469243511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469243511 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511 Building ZINC001469243511 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469243511 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 926) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCc2nc[nH]c2[C@@H]1c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001469243511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469243511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001469243511 none O=C(N1CCc2nc[nH]c2[C@@H]1c1ccc(Br)cc1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 8, 1, 8, 6, 1, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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, 4, 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] 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: [9, 2, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 19, 19, 16, 19, 19, 19, 1, 1, 1, 5, 5, 1, 2, 5, 5, 15, 15, 15, 15, 15, 19, 19, 19, 19, 5, 5, 5, 5] 20 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 927) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CCc2nc[nH]c2[C@@H]1c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC001469243511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469243511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001469243511 none O=C(N1CCc2nc[nH]c2[C@@H]1c1ccc(Br)cc1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 8, 1, 8, 6, 1, 5, 7, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 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, 4, 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] 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: [9, 2, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 18, 18, 13, 18, 18, 18, 1, 1, 1, 6, 6, 1, 1, 6, 6, 13, 13, 13, 13, 13, 18, 18, 18, 18, 6, 6, 6, 6] 20 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 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/6899/xaj-8058088.10/working/building/ZINC001469243511 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469243511 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469243511 Building ZINC001469421598 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469421598 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/928 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](CC(=O)NCc3ccc(F)cc3)C2)cc1Cl) `ZINC001469421598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469421598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001469421598 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](CC(=O)NCc3ccc(F)cc3)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', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 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, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 2, 3, 4, 6, 6, 6, 6, 6, 6, 13, 18, 18, 18, 24, 24, 24, 24, 24, 24, 24, 6, 4, 4, 4, 7, 7, 7, 4, 4, 6, 6, 6, 6, 6, 6, 13, 13, 18, 24, 24, 24, 24, 24, 24, 6, 6, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/929 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](CC(=O)NCc3ccc(F)cc3)C2)cc1Cl) `ZINC001469421598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469421598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001469421598 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](CC(=O)NCc3ccc(F)cc3)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', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 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, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 9, 14, 14, 14, 24, 24, 24, 24, 24, 24, 24, 4, 5, 5, 5, 12, 12, 12, 5, 5, 4, 4, 4, 4, 4, 4, 9, 9, 14, 24, 24, 24, 24, 24, 24, 4, 4, 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: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469421598 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598 Building ZINC001469421598 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469421598 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 928) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](CC(=O)NCc3ccc(F)cc3)C2)cc1Cl) `ZINC001469421598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469421598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001469421598 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](CC(=O)NCc3ccc(F)cc3)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', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 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, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 2, 4, 4, 1, 1, 1, 2, 3, 4, 6, 6, 6, 6, 6, 6, 13, 18, 18, 18, 24, 24, 24, 24, 24, 24, 24, 6, 4, 4, 4, 7, 7, 7, 4, 4, 6, 6, 6, 6, 6, 6, 13, 13, 18, 24, 24, 24, 24, 24, 24, 6, 6, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 929) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](CC(=O)NCc3ccc(F)cc3)C2)cc1Cl) `ZINC001469421598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469421598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001469421598 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](CC(=O)NCc3ccc(F)cc3)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', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 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, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 9, 14, 14, 14, 24, 24, 24, 24, 24, 24, 24, 4, 5, 5, 5, 12, 12, 12, 5, 5, 4, 4, 4, 4, 4, 4, 9, 9, 14, 24, 24, 24, 24, 24, 24, 4, 4, 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: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469421598 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421598 Building ZINC001469421600 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469421600 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/930 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](CC(=O)NCc3ccc(F)cc3)C2)cc1Cl) `ZINC001469421600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469421600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001469421600 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](CC(=O)NCc3ccc(F)cc3)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', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 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, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 9, 15, 15, 15, 25, 25, 25, 25, 25, 25, 25, 4, 5, 5, 5, 12, 12, 12, 5, 5, 4, 4, 4, 4, 4, 4, 9, 9, 15, 25, 25, 25, 25, 25, 25, 4, 4, 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/931 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](CC(=O)NCc3ccc(F)cc3)C2)cc1Cl) `ZINC001469421600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469421600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001469421600 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](CC(=O)NCc3ccc(F)cc3)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', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 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, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 3, 4, 6, 6, 6, 6, 6, 6, 13, 18, 18, 18, 24, 24, 24, 24, 24, 24, 24, 6, 4, 4, 4, 8, 8, 8, 4, 4, 6, 6, 6, 6, 6, 6, 13, 13, 18, 24, 24, 24, 24, 24, 24, 6, 6, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469421600 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600 Building ZINC001469421600 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469421600 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 930) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](CC(=O)NCc3ccc(F)cc3)C2)cc1Cl) `ZINC001469421600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469421600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001469421600 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](CC(=O)NCc3ccc(F)cc3)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', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 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, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 5, 5, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 9, 15, 15, 15, 25, 25, 25, 25, 25, 25, 25, 4, 5, 5, 5, 12, 12, 12, 5, 5, 4, 4, 4, 4, 4, 4, 9, 9, 15, 25, 25, 25, 25, 25, 25, 4, 4, 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 931) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](CC(=O)NCc3ccc(F)cc3)C2)cc1Cl) `ZINC001469421600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469421600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001469421600 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](CC(=O)NCc3ccc(F)cc3)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', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 1, 1, 15, 1, 1, 5, 1, 1, 16, 7, 7, 7, 7, 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, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 3, 4, 6, 6, 6, 6, 6, 6, 13, 18, 18, 18, 24, 24, 24, 24, 24, 24, 24, 6, 4, 4, 4, 8, 8, 8, 4, 4, 6, 6, 6, 6, 6, 6, 13, 13, 18, 24, 24, 24, 24, 24, 24, 6, 6, 4] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469421600 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469421600 Building ZINC001469454995 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469454995 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/932 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[C@H](O)CC1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001469454995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469454995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001469454995 none O=C(N[C@H]1CC[C@H](O)CC1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 7, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 16, 24, 42, 42, 42, 44, 44, 44, 42, 42, 7, 7, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 42, 42, 43, 44, 130, 44, 43, 42, 42, 7, 7, 7, 7, 4, 3, 1, 3] 150 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]) total number of confs: 283 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/933 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CC[C@H](O)CC1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001469454995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469454995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001469454995 none O=C(N[C@H]1CC[C@H](O)CC1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 7, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 17, 23, 40, 40, 40, 40, 40, 41, 40, 40, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 40, 40, 40, 40, 123, 40, 40, 40, 40, 8, 8, 8, 8, 3, 3, 3, 3] 150 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]) total number of confs: 248 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469454995 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995 Building ZINC001469454995 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469454995 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 932) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@H]1CC[C@H](O)CC1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001469454995.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469454995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001469454995 none O=C(N[C@H]1CC[C@H](O)CC1)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 7, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 16, 24, 42, 42, 42, 44, 44, 44, 42, 42, 7, 7, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 42, 42, 43, 44, 130, 44, 43, 42, 42, 7, 7, 7, 7, 4, 3, 1, 3] 150 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]) total number of confs: 283 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 933) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N[C@H]1CC[C@H](O)CC1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001469454995.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469454995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001469454995 none O=C(N[C@H]1CC[C@H](O)CC1)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 7, 12, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 17, 23, 40, 40, 40, 40, 40, 41, 40, 40, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 40, 40, 40, 40, 123, 40, 40, 40, 40, 8, 8, 8, 8, 3, 3, 3, 3] 150 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]) total number of confs: 248 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469454995 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469454995 Building ZINC001469928872 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469928872 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/934 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(I)cc1F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001469928872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469928872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001469928872 none O=C(Nc1ccc(I)cc1F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 18, 1, 1, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 27, 27, 7, 27, 27, 27, 27, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 27, 27, 27, 8, 8, 8, 8] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/935 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(I)cc1F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001469928872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469928872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001469928872 none O=C(Nc1ccc(I)cc1F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 18, 1, 1, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 27, 27, 27, 8, 8, 8, 8] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469928872 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872 Building ZINC001469928872 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469928872 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 934) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(I)cc1F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001469928872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469928872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001469928872 none O=C(Nc1ccc(I)cc1F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 18, 1, 1, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 27, 27, 7, 27, 27, 27, 27, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 27, 27, 27, 8, 8, 8, 8] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 935) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(I)cc1F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001469928872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469928872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 35 natoms 34 natoms 33 natoms 32 names: ZINC001469928872 none O=C(Nc1ccc(I)cc1F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 18, 1, 1, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 27, 27, 27, 8, 8, 8, 8] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469928872 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469928872 Building ZINC001469958702 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469958702 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/936 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/936' -> `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)NCC1(NC(=O)OC(C)(C)C)CCCC1) `ZINC001469958702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469958702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001469958702 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)OC(C)(C)C)CCCC1 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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 18, 29, 29, 39, 39, 45, 45, 45, 45, 29, 29, 29, 29, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 13, 13, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 29, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/937 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/937' -> `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)NCC1(NC(=O)OC(C)(C)C)CCCC1) `ZINC001469958702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469958702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001469958702 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)OC(C)(C)C)CCCC1 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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 17, 29, 29, 38, 38, 45, 45, 45, 45, 29, 29, 29, 29, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 11, 11, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 29, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469958702 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702 Building ZINC001469958702 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469958702 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 936) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)OC(C)(C)C)CCCC1) `ZINC001469958702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469958702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001469958702 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(NC(=O)OC(C)(C)C)CCCC1 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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 18, 29, 29, 39, 39, 45, 45, 45, 45, 29, 29, 29, 29, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 13, 13, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 29, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 937) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)OC(C)(C)C)CCCC1) `ZINC001469958702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469958702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001469958702 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(NC(=O)OC(C)(C)C)CCCC1 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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 17, 29, 29, 38, 38, 45, 45, 45, 45, 29, 29, 29, 29, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 11, 11, 29, 45, 45, 45, 45, 45, 45, 45, 45, 45, 29, 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, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469958702 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469958702 Building ZINC001469969412 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469969412 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/938 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](c2cccc(F)c2)[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001469969412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469969412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001469969412 none CC(C)(C)OC(=O)N1CC[C@H](c2cccc(F)c2)[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 23, 13, 23, 13, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 25, 8, 13, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 32, 32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 25, 25, 25, 25, 2, 3, 3, 6, 3, 3, 13, 13] 100 rigid atoms, others: [22, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/939 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](c2cccc(F)c2)[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001469969412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469969412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001469969412 none CC(C)(C)OC(=O)N1CC[C@H](c2cccc(F)c2)[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 29, 29, 23, 14, 23, 14, 14, 14, 14, 14, 14, 30, 30, 30, 30, 30, 30, 7, 14, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 30, 30, 30, 30, 3, 3, 3, 6, 3, 3, 14, 14] 100 rigid atoms, others: [22, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 121 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469969412 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412 Building ZINC001469969412 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469969412 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 938) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@H](c2cccc(F)c2)[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001469969412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469969412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001469969412 none CC(C)(C)OC(=O)N1CC[C@H](c2cccc(F)c2)[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 32, 32, 32, 23, 13, 23, 13, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 25, 8, 13, 2, 1, 2, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 32, 32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 25, 25, 25, 25, 2, 3, 3, 6, 3, 3, 13, 13] 100 rigid atoms, others: [22, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 939) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CC[C@H](c2cccc(F)c2)[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1) `ZINC001469969412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469969412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001469969412 none CC(C)(C)OC(=O)N1CC[C@H](c2cccc(F)c2)[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 7, 1, 1, 1, 1, 1, 15, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 29, 29, 23, 14, 23, 14, 14, 14, 14, 14, 14, 30, 30, 30, 30, 30, 30, 7, 14, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 30, 30, 30, 30, 3, 3, 3, 6, 3, 3, 14, 14] 100 rigid atoms, others: [22, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 121 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469969412 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469969412 Building ZINC001469978038 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469978038 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/940 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1c1ccc(OC)cc1) `ZINC001469978038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469978038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001469978038 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1c1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 2, 2, 5, 9, 9, 9, 9, 17, 17, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 9, 9, 9, 11, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 11, 11, 11, 9, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/941 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1c1ccc(OC)cc1) `ZINC001469978038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469978038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001469978038 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1c1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 2, 2, 5, 9, 9, 9, 9, 16, 16, 19, 19, 19, 19, 9, 9, 9, 9, 9, 10, 10, 9, 9, 13, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 10, 10, 13, 13, 13, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469978038 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038 Building ZINC001469978038 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001469978038 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 940) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1c1ccc(OC)cc1) `ZINC001469978038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001469978038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001469978038 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1c1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 2, 2, 5, 9, 9, 9, 9, 17, 17, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 9, 9, 9, 11, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 9, 9, 11, 11, 11, 9, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 941) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1c1ccc(OC)cc1) `ZINC001469978038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001469978038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001469978038 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1c1ccc(OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 1, 1, 1, 2, 2, 5, 9, 9, 9, 9, 16, 16, 19, 19, 19, 19, 9, 9, 9, 9, 9, 10, 10, 9, 9, 13, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 10, 10, 13, 13, 13, 10, 10] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001469978038 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001469978038 Building ZINC001470152324 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001470152324 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/942 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470152324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152324 none O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 17, 34, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 14, 14, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 2, 1, 2] 50 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, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/943 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470152324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152324 none O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 17, 34, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 14, 14, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 2, 1, 2] 50 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, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/944 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/944' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152324.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001470152324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152324 none O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 15, 34, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 2, 1, 2] 50 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, 42, 43]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/945 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/945' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152324.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001470152324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152324 none O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 15, 34, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 2, 1, 2] 50 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, 42, 43]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470152324 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 Building ZINC001470152324 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001470152324 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 942) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470152324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152324 none O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 17, 34, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 14, 14, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 2, 1, 2] 50 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, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 943) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470152324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152324 none O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 17, 34, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 14, 14, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 2, 1, 2] 50 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, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 944) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152324.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001470152324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152324 none O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 15, 34, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 2, 1, 2] 50 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, 42, 43]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 945) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152324.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001470152324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152324 none O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 15, 34, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 2, 1, 2] 50 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, 42, 43]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470152324 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 Building ZINC001470152324 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001470152324 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 942) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470152324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152324 none O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 17, 34, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 14, 14, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 2, 1, 2] 50 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, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 943) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470152324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152324 none O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 17, 34, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 14, 14, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 2, 1, 2] 50 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, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 944) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152324.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001470152324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152324 none O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 15, 34, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 2, 1, 2] 50 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, 42, 43]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 945) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152324.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001470152324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152324 none O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 15, 34, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 2, 1, 2] 50 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, 42, 43]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470152324 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 Building ZINC001470152324 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001470152324 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 942) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152324.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470152324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152324 none O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 17, 34, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 14, 14, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 2, 1, 2] 50 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, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 943) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152324.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470152324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152324 none O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 17, 34, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 14, 14, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 2, 1, 2] 50 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, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 944) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152324.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001470152324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152324 none O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 15, 34, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 2, 1, 2] 50 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, 42, 43]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 945) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152324.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001470152324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152324 none O=C(NC[C@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 15, 34, 34, 34, 34, 50, 50, 34, 34, 50, 50, 34, 34, 34, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 13, 13, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 2, 1, 2] 50 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, 42, 43]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470152324 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152324 Building ZINC001470152325 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001470152325 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/946 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470152325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152325 none O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 18, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 13, 13, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 3, 1, 3] 50 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, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/947 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470152325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152325 none O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 18, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 13, 13, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 3, 1, 3] 50 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, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/948 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/948' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152325.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001470152325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152325 none O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 19, 32, 32, 32, 32, 50, 50, 32, 32, 50, 50, 32, 32, 32, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 15, 15, 32, 32, 50, 50, 50, 50, 32, 32, 32, 32, 2, 1, 2] 50 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, 42, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/949 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/949' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152325.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001470152325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152325 none O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 19, 32, 32, 32, 32, 50, 50, 32, 32, 50, 50, 32, 32, 32, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 15, 15, 32, 32, 50, 50, 50, 50, 32, 32, 32, 32, 2, 1, 2] 50 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, 42, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470152325 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 Building ZINC001470152325 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001470152325 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 946) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470152325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152325 none O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 18, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 13, 13, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 3, 1, 3] 50 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, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 947) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470152325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152325 none O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 18, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 13, 13, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 3, 1, 3] 50 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, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 948) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152325.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001470152325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152325 none O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 19, 32, 32, 32, 32, 50, 50, 32, 32, 50, 50, 32, 32, 32, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 15, 15, 32, 32, 50, 50, 50, 50, 32, 32, 32, 32, 2, 1, 2] 50 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, 42, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 949) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152325.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001470152325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152325 none O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 19, 32, 32, 32, 32, 50, 50, 32, 32, 50, 50, 32, 32, 32, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 15, 15, 32, 32, 50, 50, 50, 50, 32, 32, 32, 32, 2, 1, 2] 50 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, 42, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470152325 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 Building ZINC001470152325 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001470152325 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 946) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470152325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152325 none O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 18, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 13, 13, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 3, 1, 3] 50 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, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 947) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470152325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152325 none O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 18, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 13, 13, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 3, 1, 3] 50 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, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 948) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152325.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001470152325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152325 none O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 19, 32, 32, 32, 32, 50, 50, 32, 32, 50, 50, 32, 32, 32, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 15, 15, 32, 32, 50, 50, 50, 50, 32, 32, 32, 32, 2, 1, 2] 50 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, 42, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 949) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152325.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001470152325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152325 none O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 19, 32, 32, 32, 32, 50, 50, 32, 32, 50, 50, 32, 32, 32, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 15, 15, 32, 32, 50, 50, 50, 50, 32, 32, 32, 32, 2, 1, 2] 50 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, 42, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470152325 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 Building ZINC001470152325 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001470152325 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 946) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470152325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152325 none O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 18, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 13, 13, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 3, 1, 3] 50 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, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 947) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470152325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152325 none O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 18, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 34, 34, 34, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 2, 13, 13, 34, 34, 50, 50, 50, 50, 34, 34, 34, 34, 3, 1, 3] 50 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, 42, 43]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 948) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152325.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001470152325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152325 none O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 19, 32, 32, 32, 32, 50, 50, 32, 32, 50, 50, 32, 32, 32, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 15, 15, 32, 32, 50, 50, 50, 50, 32, 32, 32, 32, 2, 1, 2] 50 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, 42, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 949) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001470152325.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001470152325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001470152325 none O=C(NC[C@@H]1CN(c2ccc(Cl)cc2)CCO1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 8, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 6, 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, 7, 7, 7, 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, 7, 7] 0 hydrogens need 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, 19, 32, 32, 32, 32, 50, 50, 32, 32, 50, 50, 32, 32, 32, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 3, 15, 15, 32, 32, 50, 50, 50, 50, 32, 32, 32, 32, 2, 1, 2] 50 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, 42, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470152325 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470152325 Building ZINC001470575850 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470575850 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/950 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccnc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4cc(Cl)cc(Cl)c4)CC3)n2)cn1) `ZINC001470575850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470575850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001470575850 none Cn1cc(c2ccnc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4cc(Cl)cc(Cl)c4)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', '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', 'C.3', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 29, 29, 29, 29, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29, 50, 50, 50, 50, 50, 50, 29, 29, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5, 5, 50] 50 rigid atoms, others: [41, 42, 43, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/951 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(c2ccnc(C3CCN(C(=O)[C@]([O-])([SiH3])c4cc(Cl)cc(Cl)c4)CC3)n2)cn1) `ZINC001470575850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470575850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001470575850 none Cn1cc(c2ccnc(C3CCN(C(=O)[C@]([O-])([SiH3])c4cc(Cl)cc(Cl)c4)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', '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', 'C.3', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 34, 34, 34, 34, 34, 5, 5, 5, 5, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 34, 50, 50, 50, 50, 50, 50, 34, 34, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5, 5, 50] 50 rigid atoms, others: [41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470575850 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850 Building ZINC001470575850 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470575850 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 950) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cn1cc(c2ccnc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4cc(Cl)cc(Cl)c4)CC3)n2)cn1) `ZINC001470575850.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470575850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001470575850 none Cn1cc(c2ccnc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4cc(Cl)cc(Cl)c4)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', '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', 'C.3', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 29, 29, 29, 29, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29, 50, 50, 50, 50, 50, 50, 29, 29, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5, 5, 50] 50 rigid atoms, others: [41, 42, 43, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 951) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cn1cc(c2ccnc(C3CCN(C(=O)[C@]([O-])([SiH3])c4cc(Cl)cc(Cl)c4)CC3)n2)cn1) `ZINC001470575850.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470575850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001470575850 none Cn1cc(c2ccnc(C3CCN(C(=O)[C@]([O-])([SiH3])c4cc(Cl)cc(Cl)c4)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', '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', 'C.3', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 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, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 34, 34, 34, 34, 34, 5, 5, 5, 5, 3, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 34, 50, 50, 50, 50, 50, 50, 34, 34, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5, 5, 5, 50] 50 rigid atoms, others: [41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470575850 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470575850 Building ZINC001470843707 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470843707 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/952 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@H]21) `ZINC001470843707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470843707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001470843707 none CC(C)(C)OC(=O)N1CCC[C@@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 18, 29, 18, 18, 18, 18, 18, 18, 4, 18, 4, 1, 4, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 18, 18, 18, 18, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 18, 18, 18, 18, 18, 18, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/953 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]2[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@H]21) `ZINC001470843707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470843707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001470843707 none CC(C)(C)OC(=O)N1CCC[C@@H]2[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 18, 28, 18, 18, 18, 18, 18, 18, 4, 18, 4, 1, 4, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 18, 18, 18, 18, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 18, 18, 18, 18, 18, 18, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470843707 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707 Building ZINC001470843707 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470843707 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 952) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCC[C@@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@H]21) `ZINC001470843707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470843707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001470843707 none CC(C)(C)OC(=O)N1CCC[C@@H]2[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 18, 29, 18, 18, 18, 18, 18, 18, 4, 18, 4, 1, 4, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 18, 18, 18, 18, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 18, 18, 18, 18, 18, 18, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 953) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCC[C@@H]2[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@H]21) `ZINC001470843707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470843707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001470843707 none CC(C)(C)OC(=O)N1CCC[C@@H]2[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 18, 28, 18, 18, 18, 18, 18, 18, 4, 18, 4, 1, 4, 1, 1, 1, 6, 6, 10, 10, 6, 10, 10, 10, 18, 18, 18, 18, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 18, 18, 18, 18, 18, 18, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470843707 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843707 Building ZINC001470843710 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470843710 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/954 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]2[C@@H]1C(C)(C)[C@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001470843710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470843710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001470843710 none CC(C)(C)OC(=O)N1CCC[C@H]2[C@@H]1C(C)(C)[C@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 17, 24, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 17, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/955 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@H]2[C@@H]1C(C)(C)[C@H]2NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001470843710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470843710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001470843710 none CC(C)(C)OC(=O)N1CCC[C@H]2[C@@H]1C(C)(C)[C@H]2NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 16, 24, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 16, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470843710 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710 Building ZINC001470843710 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470843710 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 954) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCC[C@H]2[C@@H]1C(C)(C)[C@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001470843710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470843710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001470843710 none CC(C)(C)OC(=O)N1CCC[C@H]2[C@@H]1C(C)(C)[C@H]2NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 17, 24, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 17, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 955) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCC[C@H]2[C@@H]1C(C)(C)[C@H]2NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC001470843710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470843710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC001470843710 none CC(C)(C)OC(=O)N1CCC[C@H]2[C@@H]1C(C)(C)[C@H]2NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 16, 24, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 16, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470843710 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843710 Building ZINC001470843712 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470843712 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/956 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@@H]21) `ZINC001470843712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470843712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001470843712 none CC(C)(C)OC(=O)N1CCC[C@@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 22, 14, 14, 14, 14, 14, 14, 7, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/957 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@@H]21) `ZINC001470843712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470843712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001470843712 none CC(C)(C)OC(=O)N1CCC[C@@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 20, 13, 13, 13, 13, 13, 13, 6, 13, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470843712 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712 Building ZINC001470843712 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470843712 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 956) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCC[C@@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@@H]21) `ZINC001470843712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470843712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001470843712 none CC(C)(C)OC(=O)N1CCC[C@@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 22, 14, 14, 14, 14, 14, 14, 7, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 14, 14, 14, 14, 14, 14, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 957) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCC[C@@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@@H]21) `ZINC001470843712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470843712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001470843712 none CC(C)(C)OC(=O)N1CCC[C@@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 20, 13, 13, 13, 13, 13, 13, 6, 13, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470843712 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843712 Building ZINC001470843714 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470843714 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/958 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@H]21) `ZINC001470843714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470843714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001470843714 none CC(C)(C)OC(=O)N1CCC[C@@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 14, 23, 14, 14, 14, 14, 14, 14, 4, 14, 4, 1, 4, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 14, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/959 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC[C@@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@H]21) `ZINC001470843714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470843714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001470843714 none CC(C)(C)OC(=O)N1CCC[C@@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 21, 14, 21, 14, 14, 14, 14, 14, 14, 4, 14, 4, 1, 4, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 14, 14, 14, 14, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 14, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470843714 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714 Building ZINC001470843714 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001470843714 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 958) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCC[C@@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@H]21) `ZINC001470843714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001470843714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001470843714 none CC(C)(C)OC(=O)N1CCC[C@@H]2[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 14, 23, 14, 14, 14, 14, 14, 14, 4, 14, 4, 1, 4, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 14, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 959) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)N1CCC[C@@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@H]21) `ZINC001470843714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001470843714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001470843714 none CC(C)(C)OC(=O)N1CCC[C@@H]2[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C(C)(C)[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 21, 14, 21, 14, 14, 14, 14, 14, 14, 4, 14, 4, 1, 4, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 14, 14, 14, 14, 14, 29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 14, 14, 14, 14, 14, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001470843714 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001470843714 Building ZINC001471001462 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471001462 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/960 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccn(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2F)n1) `ZINC001471001462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471001462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001471001462 none CCOC(=O)c1ccn(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', '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, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 8, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 26, 28, 26, 26, 26, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 26, 32, 32, 32, 32, 32, 26, 26, 11, 11, 3, 4, 4, 4, 4, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/961 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1ccn(c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2F)n1) `ZINC001471001462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471001462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001471001462 none CCOC(=O)c1ccn(c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', '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, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 8, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 26, 28, 26, 26, 26, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 26, 33, 33, 33, 33, 33, 26, 26, 11, 11, 3, 4, 4, 4, 4, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471001462 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462 Building ZINC001471001462 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471001462 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 960) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1ccn(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2F)n1) `ZINC001471001462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471001462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001471001462 none CCOC(=O)c1ccn(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', '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, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 8, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 26, 28, 26, 26, 26, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 26, 32, 32, 32, 32, 32, 26, 26, 11, 11, 3, 4, 4, 4, 4, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 961) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)c1ccn(c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2F)n1) `ZINC001471001462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471001462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001471001462 none CCOC(=O)c1ccn(c2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4cc(F)ccc43)cc2F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', '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, 1, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 15, 8, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 26, 28, 26, 26, 26, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 26, 33, 33, 33, 33, 33, 26, 26, 11, 11, 3, 4, 4, 4, 4, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471001462 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471001462 Building ZINC001471042950 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471042950 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/962 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(O)(c2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001471042950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471042950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471042950 none O=C(N1CC(O)(c2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 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: [2, 1, 3, 12, 12, 12, 12, 50, 50, 35, 50, 50, 50, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 12, 12, 36, 50, 50, 50, 50, 12, 12, 2, 2, 2] 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]) total number of confs: 174 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/963 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(O)(c2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001471042950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471042950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471042950 none O=C(N1CC(O)(c2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 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: [2, 1, 3, 11, 11, 11, 11, 50, 50, 27, 50, 50, 50, 11, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 33, 50, 50, 50, 50, 11, 11, 3, 1, 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]) total number of confs: 187 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471042950 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950 Building ZINC001471042950 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471042950 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 962) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CC(O)(c2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001471042950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471042950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471042950 none O=C(N1CC(O)(c2cccc(Br)c2)C1)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 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: [2, 1, 3, 12, 12, 12, 12, 50, 50, 35, 50, 50, 50, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 12, 12, 36, 50, 50, 50, 50, 12, 12, 2, 2, 2] 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]) total number of confs: 174 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 963) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(N1CC(O)(c2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001471042950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471042950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471042950 none O=C(N1CC(O)(c2cccc(Br)c2)C1)[C@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 1, 1, 1, 1, 1, 17, 1, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 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: [2, 1, 3, 11, 11, 11, 11, 50, 50, 27, 50, 50, 50, 11, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 11, 11, 33, 50, 50, 50, 50, 11, 11, 3, 1, 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]) total number of confs: 187 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471042950 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471042950 Building ZINC001471157886 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471157886 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/964 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H](Cc1ccccc1)NC(=O)OC(C)(C)C) `ZINC001471157886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471157886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001471157886 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H](Cc1ccccc1)NC(=O)OC(C)(C)C 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 12, 13, 22, 22, 32, 32, 32, 32, 32, 32, 22, 35, 49, 49, 49, 49, 49, 49, 2, 2, 2, 2, 2, 2, 3, 12, 12, 14, 14, 32, 32, 32, 32, 32, 32, 32, 35, 49, 49, 49, 49, 49, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/965 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H](Cc1ccccc1)NC(=O)OC(C)(C)C) `ZINC001471157886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471157886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001471157886 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H](Cc1ccccc1)NC(=O)OC(C)(C)C 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 11, 20, 20, 31, 31, 31, 31, 31, 31, 20, 32, 48, 48, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2, 3, 9, 9, 11, 11, 31, 31, 31, 31, 31, 31, 31, 32, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471157886 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886 Building ZINC001471157886 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471157886 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 964) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H](Cc1ccccc1)NC(=O)OC(C)(C)C) `ZINC001471157886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471157886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001471157886 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@@H](Cc1ccccc1)NC(=O)OC(C)(C)C 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 12, 13, 22, 22, 32, 32, 32, 32, 32, 32, 22, 35, 49, 49, 49, 49, 49, 49, 2, 2, 2, 2, 2, 2, 3, 12, 12, 14, 14, 32, 32, 32, 32, 32, 32, 32, 35, 49, 49, 49, 49, 49, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 965) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H](Cc1ccccc1)NC(=O)OC(C)(C)C) `ZINC001471157886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471157886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001471157886 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC[C@@H](Cc1ccccc1)NC(=O)OC(C)(C)C 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 11, 20, 20, 31, 31, 31, 31, 31, 31, 20, 32, 48, 48, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2, 3, 9, 9, 11, 11, 31, 31, 31, 31, 31, 31, 31, 32, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471157886 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157886 Building ZINC001471157887 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471157887 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/966 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@H](Cc1ccccc1)NC(=O)OC(C)(C)C) `ZINC001471157887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471157887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001471157887 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@H](Cc1ccccc1)NC(=O)OC(C)(C)C 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 11, 18, 18, 29, 29, 29, 29, 29, 29, 18, 30, 46, 46, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2, 3, 9, 9, 11, 11, 29, 29, 29, 29, 29, 29, 29, 30, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/967 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC[C@H](Cc1ccccc1)NC(=O)OC(C)(C)C) `ZINC001471157887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471157887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001471157887 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC[C@H](Cc1ccccc1)NC(=O)OC(C)(C)C 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 11, 13, 21, 21, 31, 31, 31, 31, 31, 31, 21, 33, 47, 47, 49, 49, 49, 49, 2, 2, 2, 2, 2, 2, 3, 11, 11, 13, 13, 31, 31, 31, 31, 31, 31, 31, 33, 49, 49, 49, 49, 49, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471157887 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887 Building ZINC001471157887 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471157887 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 966) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@H](Cc1ccccc1)NC(=O)OC(C)(C)C) `ZINC001471157887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471157887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001471157887 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NCC[C@H](Cc1ccccc1)NC(=O)OC(C)(C)C 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 9, 11, 18, 18, 29, 29, 29, 29, 29, 29, 18, 30, 46, 46, 48, 48, 48, 48, 2, 2, 2, 2, 2, 2, 3, 9, 9, 11, 11, 29, 29, 29, 29, 29, 29, 29, 30, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 967) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC[C@H](Cc1ccccc1)NC(=O)OC(C)(C)C) `ZINC001471157887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471157887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001471157887 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NCC[C@H](Cc1ccccc1)NC(=O)OC(C)(C)C 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', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 11, 13, 21, 21, 31, 31, 31, 31, 31, 31, 21, 33, 47, 47, 49, 49, 49, 49, 2, 2, 2, 2, 2, 2, 3, 11, 11, 13, 13, 31, 31, 31, 31, 31, 31, 31, 33, 49, 49, 49, 49, 49, 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, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471157887 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471157887 Building ZINC001471249821 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471249821 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/968 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc21)C(F)(F)F) `ZINC001471249821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471249821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471249821 none O=C(NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 12, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 38, 38, 38, 38, 38, 20, 20, 12, 12, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/969 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc21)C(F)(F)F) `ZINC001471249821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471249821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471249821 none O=C(NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 11, 5, 5, 5, 5, 3, 2, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 16, 16, 11, 11, 5, 5, 3, 3, 3, 3, 5, 5, 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, 46, 47, 48]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471249821 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821 Building ZINC001471249821 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471249821 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 968) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc21)C(F)(F)F) `ZINC001471249821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471249821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471249821 none O=C(NCC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 12, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 38, 38, 38, 38, 38, 20, 20, 12, 12, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 969) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc21)C(F)(F)F) `ZINC001471249821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471249821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471249821 none O=C(NCC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 11, 5, 5, 5, 5, 3, 2, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 16, 16, 11, 11, 5, 5, 3, 3, 3, 3, 5, 5, 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, 46, 47, 48]) total number of confs: 119 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471249821 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249821 Building ZINC001471249822 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471249822 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/970 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc21)C(F)(F)F) `ZINC001471249822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471249822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471249822 none O=C(NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 15, 11, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 15, 15, 11, 11, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/971 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc21)C(F)(F)F) `ZINC001471249822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471249822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471249822 none O=C(NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 11, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 38, 38, 38, 38, 38, 18, 18, 11, 11, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/6899/xaj-8058088.10/working/building/ZINC001471249822 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471249822 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822 Building ZINC001471249822 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471249822 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 970) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc21)C(F)(F)F) `ZINC001471249822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471249822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471249822 none O=C(NCC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 15, 11, 4, 4, 4, 4, 3, 2, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 15, 15, 11, 11, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 116 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 971) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc21)C(F)(F)F) `ZINC001471249822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471249822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001471249822 none O=C(NCC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3cc(F)ccc32)c2ccccc21)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 11, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 38, 38, 38, 38, 38, 18, 18, 11, 11, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/6899/xaj-8058088.10/working/building/ZINC001471249822 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471249822 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471249822 Building ZINC001471612080 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471612080 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/972 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1nc2c(s1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C2) `ZINC001471612080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471612080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001471612080 none CC(C)(C)OC(=O)NCc1nc2c(s1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 14, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 44, 35, 44, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 47, 47, 47, 47, 47, 47, 47, 47, 47, 35, 22, 22, 4, 4, 4, 4, 2, 2, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/973 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1nc2c(s1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C2) `ZINC001471612080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471612080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001471612080 none CC(C)(C)OC(=O)NCc1nc2c(s1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 14, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 44, 34, 44, 21, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 47, 47, 47, 47, 47, 47, 47, 47, 47, 34, 21, 21, 4, 4, 4, 4, 2, 2, 4, 4] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471612080 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080 Building ZINC001471612080 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471612080 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 972) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1nc2c(s1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C2) `ZINC001471612080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471612080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001471612080 none CC(C)(C)OC(=O)NCc1nc2c(s1)CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 14, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 44, 35, 44, 22, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 47, 47, 47, 47, 47, 47, 47, 47, 47, 35, 22, 22, 4, 4, 4, 4, 2, 2, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 973) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCc1nc2c(s1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C2) `ZINC001471612080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471612080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001471612080 none CC(C)(C)OC(=O)NCc1nc2c(s1)CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 14, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 44, 34, 44, 21, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 2, 4, 47, 47, 47, 47, 47, 47, 47, 47, 47, 34, 21, 21, 4, 4, 4, 4, 2, 2, 4, 4] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471612080 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471612080 Building ZINC001471613694 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471613694 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/974 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCO2) `ZINC001471613694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471613694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001471613694 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 7, 7, 7, 7] 0 hydrogens 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, 20, 27, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/975 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCO2) `ZINC001471613694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471613694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001471613694 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 30, 22, 30, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 3, 5, 5, 5, 40, 40, 40, 40, 40, 40, 40, 40, 40, 22, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471613694 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694 Building ZINC001471613694 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471613694 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 974) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)Nc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCO2) `ZINC001471613694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471613694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001471613694 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 7, 7, 7, 7] 0 hydrogens 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, 20, 27, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 975) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)Nc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCO2) `ZINC001471613694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471613694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001471613694 none CC(C)(C)OC(=O)Nc1ccc2c(c1)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', '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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 30, 22, 30, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 3, 5, 5, 5, 40, 40, 40, 40, 40, 40, 40, 40, 40, 22, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5] 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471613694 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471613694 Building ZINC001471657320 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471657320 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/976 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1Cc2cc(F)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001471657320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471657320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471657320 none CCOC(=O)[C@@H]1Cc2cc(F)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', '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, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 9, 32, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 9, 1, 1, 1, 4, 4, 4, 4, 4, 9, 32, 32, 32, 32, 32, 9, 9, 9, 9, 9, 4, 4, 9, 9] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/977 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1Cc2cc(F)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001471657320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471657320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471657320 none CCOC(=O)[C@@H]1Cc2cc(F)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', '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, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 31, 31, 7, 31, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 1, 1, 1, 3, 3, 3, 3, 3, 7, 33, 33, 33, 33, 33, 7, 7, 7, 7, 7, 3, 3, 7, 7] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471657320 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320 Building ZINC001471657320 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471657320 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 976) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)[C@@H]1Cc2cc(F)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001471657320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471657320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471657320 none CCOC(=O)[C@@H]1Cc2cc(F)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', '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, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 9, 32, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 9, 1, 1, 1, 4, 4, 4, 4, 4, 9, 32, 32, 32, 32, 32, 9, 9, 9, 9, 9, 4, 4, 9, 9] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 977) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)[C@@H]1Cc2cc(F)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001471657320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471657320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471657320 none CCOC(=O)[C@@H]1Cc2cc(F)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', '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, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 31, 31, 7, 31, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 1, 1, 1, 3, 3, 3, 3, 3, 7, 33, 33, 33, 33, 33, 7, 7, 7, 7, 7, 3, 3, 7, 7] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 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]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471657320 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657320 Building ZINC001471657321 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471657321 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/978 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1Cc2cc(F)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001471657321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471657321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471657321 none CCOC(=O)[C@H]1Cc2cc(F)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', '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, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 31, 31, 7, 31, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 7, 33, 33, 33, 33, 33, 7, 7, 7, 7, 7, 4, 4, 7, 7] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/979 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1Cc2cc(F)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001471657321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471657321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471657321 none CCOC(=O)[C@H]1Cc2cc(F)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', '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, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 31, 7, 31, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 1, 1, 1, 4, 4, 4, 4, 4, 7, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 4, 4, 7, 7] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471657321 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321 Building ZINC001471657321 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471657321 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 978) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)[C@H]1Cc2cc(F)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001471657321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471657321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471657321 none CCOC(=O)[C@H]1Cc2cc(F)ccc2N(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', '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, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 31, 31, 7, 31, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 7, 33, 33, 33, 33, 33, 7, 7, 7, 7, 7, 4, 4, 7, 7] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 979) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CCOC(=O)[C@H]1Cc2cc(F)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)C1) `ZINC001471657321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471657321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001471657321 none CCOC(=O)[C@H]1Cc2cc(F)ccc2N(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)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', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', '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, 15, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 31, 7, 31, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 1, 1, 1, 4, 4, 4, 4, 4, 7, 32, 32, 32, 32, 32, 7, 7, 7, 7, 7, 4, 4, 7, 7] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471657321 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471657321 Building ZINC001471739313 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471739313 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/980 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@H]1C(F)(F)F) `ZINC001471739313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471739313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001471739313 none CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 28, 40, 13, 6, 6, 6, 6, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 13, 13, 6, 6, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 45, 12, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/981 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@H]1C(F)(F)F) `ZINC001471739313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471739313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001471739313 none CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 32, 43, 13, 6, 6, 6, 6, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 13, 13, 6, 6, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 45, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471739313 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313 Building ZINC001471739313 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471739313 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 980) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@H]1C(F)(F)F) `ZINC001471739313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471739313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001471739313 none CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 28, 40, 13, 6, 6, 6, 6, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 13, 13, 6, 6, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 45, 12, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 981) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@H]1C(F)(F)F) `ZINC001471739313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471739313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001471739313 none CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 32, 43, 13, 6, 6, 6, 6, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 13, 13, 6, 6, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 45, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471739313 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739313 Building ZINC001471739314 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471739314 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/982 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@@H]1C(F)(F)F) `ZINC001471739314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471739314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001471739314 none CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 33, 47, 12, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 12, 12, 4, 4, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 45, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/983 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@@H]1C(F)(F)F) `ZINC001471739314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471739314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001471739314 none CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 34, 46, 14, 4, 4, 4, 4, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 14, 14, 4, 4, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 45, 12, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471739314 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314 Building ZINC001471739314 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471739314 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 982) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/982: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@@H]1C(F)(F)F) `ZINC001471739314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471739314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001471739314 none CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 33, 47, 12, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 12, 12, 4, 4, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 45, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 983) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/983: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@@H]1C(F)(F)F) `ZINC001471739314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471739314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001471739314 none CC(C)(C)OC(=O)NC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 34, 46, 14, 4, 4, 4, 4, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 14, 14, 4, 4, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 45, 12, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471739314 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739314 Building ZINC001471739315 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471739315 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/984 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@@H]1C(F)(F)F) `ZINC001471739315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471739315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001471739315 none CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 31, 41, 13, 6, 6, 6, 6, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 13, 13, 6, 6, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 45, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/985 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@@H]1C(F)(F)F) `ZINC001471739315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471739315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001471739315 none CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 30, 42, 13, 6, 6, 6, 6, 1, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 13, 13, 6, 6, 2, 2, 2, 2, 6, 6] 50 rigid atoms, others: [12, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471739315 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315 Building ZINC001471739315 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471739315 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 984) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@@H]1C(F)(F)F) `ZINC001471739315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471739315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001471739315 none CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 31, 41, 13, 6, 6, 6, 6, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 13, 13, 6, 6, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [48, 45, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 985) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@@H]1C(F)(F)F) `ZINC001471739315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471739315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001471739315 none CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 30, 42, 13, 6, 6, 6, 6, 1, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 6, 6, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 13, 13, 6, 6, 2, 2, 2, 2, 6, 6] 50 rigid atoms, others: [12, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471739315 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739315 Building ZINC001471739316 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471739316 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/986 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@H]1C(F)(F)F) `ZINC001471739316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471739316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001471739316 none CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 36, 48, 14, 4, 4, 4, 4, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 14, 14, 4, 4, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 45, 12, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/987 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@H]1C(F)(F)F) `ZINC001471739316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471739316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001471739316 none CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 30, 45, 11, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 11, 11, 4, 4, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 45, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471739316 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316 Building ZINC001471739316 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471739316 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 986) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@H]1C(F)(F)F) `ZINC001471739316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471739316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001471739316 none CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 36, 48, 14, 4, 4, 4, 4, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 14, 14, 4, 4, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 45, 12, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 987) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@H]1C(F)(F)F) `ZINC001471739316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471739316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001471739316 none CC(C)(C)OC(=O)NC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)C[C@H]1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 5, 15, 15, 15, 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, 3, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 30, 45, 11, 4, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 11, 11, 4, 4, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 45, 13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471739316 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471739316 Building ZINC001471879970 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471879970 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/988 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471879970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471879970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001471879970 none O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 28, 34, 34, 32, 34, 34, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 28, 28, 34, 34, 34, 34, 34, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 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, 47, 48, 49]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/989 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471879970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471879970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001471879970 none O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 28, 34, 34, 32, 34, 34, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 28, 28, 34, 34, 34, 34, 34, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 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, 47, 48, 49]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/990 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/990' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471879970.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471879970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001471879970 none O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 15, 29, 34, 34, 31, 34, 34, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 29, 29, 34, 34, 34, 34, 34, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 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, 47, 48, 49]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/991 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/991' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471879970.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471879970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001471879970 none O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 15, 29, 34, 34, 31, 34, 34, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 29, 29, 34, 34, 34, 34, 34, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 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, 47, 48, 49]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471879970 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 Building ZINC001471879970 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471879970 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 988) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471879970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471879970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001471879970 none O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 28, 34, 34, 32, 34, 34, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 28, 28, 34, 34, 34, 34, 34, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 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, 47, 48, 49]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 989) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471879970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471879970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001471879970 none O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 28, 34, 34, 32, 34, 34, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 28, 28, 34, 34, 34, 34, 34, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 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, 47, 48, 49]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 990) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471879970.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471879970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001471879970 none O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 15, 29, 34, 34, 31, 34, 34, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 29, 29, 34, 34, 34, 34, 34, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 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, 47, 48, 49]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 991) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471879970.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471879970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001471879970 none O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 15, 29, 34, 34, 31, 34, 34, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 29, 29, 34, 34, 34, 34, 34, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 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, 47, 48, 49]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471879970 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 Building ZINC001471879970 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471879970 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 988) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471879970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471879970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001471879970 none O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 28, 34, 34, 32, 34, 34, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 28, 28, 34, 34, 34, 34, 34, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 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, 47, 48, 49]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 989) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471879970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471879970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001471879970 none O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 28, 34, 34, 32, 34, 34, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 28, 28, 34, 34, 34, 34, 34, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 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, 47, 48, 49]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 990) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471879970.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471879970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001471879970 none O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 15, 29, 34, 34, 31, 34, 34, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 29, 29, 34, 34, 34, 34, 34, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 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, 47, 48, 49]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 991) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471879970.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471879970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001471879970 none O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 15, 29, 34, 34, 31, 34, 34, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 29, 29, 34, 34, 34, 34, 34, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 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, 47, 48, 49]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471879970 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 Building ZINC001471879970 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001471879970 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 988) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471879970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471879970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001471879970 none O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 28, 34, 34, 32, 34, 34, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 28, 28, 34, 34, 34, 34, 34, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 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, 47, 48, 49]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 989) grep: /scratch/xiaobo/6899/xaj-8058088.10/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(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471879970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471879970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001471879970 none O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 28, 34, 34, 32, 34, 34, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 28, 28, 34, 34, 34, 34, 34, 14, 14, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 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, 47, 48, 49]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `2' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/2 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 2 (index: 990) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471879970.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001471879970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001471879970 none O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 15, 29, 34, 34, 31, 34, 34, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 29, 29, 34, 34, 34, 34, 34, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 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, 47, 48, 49]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `3' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/3 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 3 (index: 991) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001471879970.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001471879970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001471879970 none O=C(N[C@@H]1CN(Cc2ccccc2)C[C@H]1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 15, 29, 34, 34, 31, 34, 34, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 29, 29, 34, 34, 34, 34, 34, 15, 15, 4, 4, 4, 4] 50 rigid atoms, others: [1, 21, 22, 23] set([0, 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, 47, 48, 49]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471879970 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 2: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/2.* 3: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/3.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471879970 Building ZINC001471925218 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471925218 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/992 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2Cc3cc(Br)ccc3OC3(CCC3)C2)cn1) `ZINC001471925218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471925218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471925218 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2Cc3cc(Br)ccc3OC3(CCC3)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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 12, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/993 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2Cc3cc(Br)ccc3OC3(CCC3)C2)cn1) `ZINC001471925218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471925218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471925218 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2Cc3cc(Br)ccc3OC3(CCC3)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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 7, 7, 6, 6, 1, 1, 1, 1, 12, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 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: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471925218 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218 Building ZINC001471925218 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471925218 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 992) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2Cc3cc(Br)ccc3OC3(CCC3)C2)cn1) `ZINC001471925218.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471925218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471925218 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2Cc3cc(Br)ccc3OC3(CCC3)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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 12, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 993) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2Cc3cc(Br)ccc3OC3(CCC3)C2)cn1) `ZINC001471925218.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471925218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001471925218 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2Cc3cc(Br)ccc3OC3(CCC3)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.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 7, 7, 6, 6, 1, 1, 1, 1, 12, 15, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 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: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471925218 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471925218 Building ZINC001471956784 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471956784 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/994 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Br)cc(Br)c2N)c1) `ZINC001471956784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471956784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001471956784 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Br)cc(Br)c2N)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 26, 26, 26, 21, 26, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 3, 11, 11, 26, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 93 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/995 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NCc2cc(Br)cc(Br)c2N)c1) `ZINC001471956784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471956784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001471956784 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCc2cc(Br)cc(Br)c2N)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 3, 3, 3, 11, 26, 26, 26, 22, 26, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 26, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 82 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471956784 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784 Building ZINC001471956784 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471956784 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 994) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Br)cc(Br)c2N)c1) `ZINC001471956784.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471956784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001471956784 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NCc2cc(Br)cc(Br)c2N)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 26, 26, 26, 21, 26, 26, 26, 26, 4, 4, 4, 4, 2, 4, 4, 3, 11, 11, 26, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 93 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 995) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: Cc1cccc([C@]([O-])([SiH3])C(=O)NCc2cc(Br)cc(Br)c2N)c1) `ZINC001471956784.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471956784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001471956784 none Cc1cccc([C@]([O-])([SiH3])C(=O)NCc2cc(Br)cc(Br)c2N)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.pl3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 1, 3, 3, 3, 11, 26, 26, 26, 22, 26, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 26, 26, 26, 26, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 82 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471956784 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471956784 Building ZINC001471974841 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471974841 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/996 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C(F)(F)F)c(I)c1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471974841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471974841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471974841 none O=C(Nc1ccc(C(F)(F)F)c(I)c1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'I', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 18, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 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: [10, 1, 10, 10, 48, 48, 38, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 48, 48, 48, 6, 6, 12, 6, 6] 100 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/997 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc(C(F)(F)F)c(I)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471974841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471974841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471974841 none O=C(Nc1ccc(C(F)(F)F)c(I)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'I', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 18, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 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: [10, 1, 10, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 48, 48, 48, 6, 6, 12, 6, 6] 100 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471974841 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841 Building ZINC001471974841 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001471974841 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 996) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(C(F)(F)F)c(I)c1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471974841.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001471974841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471974841 none O=C(Nc1ccc(C(F)(F)F)c(I)c1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'I', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 18, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 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: [10, 1, 10, 10, 48, 48, 38, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 48, 48, 48, 6, 6, 12, 6, 6] 100 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]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 997) grep: /scratch/xiaobo/6899/xaj-8058088.10/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: O=C(Nc1ccc(C(F)(F)F)c(I)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001471974841.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001471974841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001471974841 none O=C(Nc1ccc(C(F)(F)F)c(I)c1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'I', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 18, 1, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 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: [10, 1, 10, 10, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 6, 6, 1, 1, 6, 6, 10, 48, 48, 48, 6, 6, 12, 6, 6] 100 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001471974841 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001471974841 Building ZINC001472159493 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472159493 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/998 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1(c2ccccc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001472159493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472159493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001472159493 none CC(C)(C)OC(=O)NCC1(c2ccccc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 49, 31, 49, 11, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 11, 11, 10, 10, 4, 10, 10, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4, 4, 4] 100 rigid atoms, others: [54, 57, 56, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 55, 58, 59, 60, 61]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/999 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1(c2ccccc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001472159493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472159493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001472159493 none CC(C)(C)OC(=O)NCC1(c2ccccc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 35, 48, 12, 4, 4, 4, 9, 9, 5, 9, 9, 4, 4, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 12, 12, 9, 9, 4, 9, 9, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4, 4, 4] 100 rigid atoms, others: [54, 57, 56, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 55, 58, 59, 60, 61]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001472159493 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493 Building ZINC001472159493 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001472159493 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 998) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1(c2ccccc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001472159493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472159493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001472159493 none CC(C)(C)OC(=O)NCC1(c2ccccc2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 49, 31, 49, 11, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 11, 11, 10, 10, 4, 10, 10, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4, 4, 4] 100 rigid atoms, others: [54, 57, 56, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 55, 58, 59, 60, 61]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 mkdir: created directory `1' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493/1 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 1 (index: 999) grep: /scratch/xiaobo/6899/xaj-8058088.10/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1(c2ccccc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1) `ZINC001472159493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001472159493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001472159493 none CC(C)(C)OC(=O)NCC1(c2ccccc2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 48, 35, 48, 12, 4, 4, 4, 9, 9, 5, 9, 9, 4, 4, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 12, 12, 9, 9, 4, 9, 9, 4, 4, 4, 4, 1, 1, 2, 1, 1, 4, 4, 4, 4] 100 rigid atoms, others: [54, 57, 56, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 55, 58, 59, 60, 61]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001472159493 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 1: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493/1.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472159493 Building ZINC001472351939 mkdir: created directory `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472351939' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472351939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001472351939 mkdir: created directory `0' /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472351939/0 /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472351939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/6899/xaj-8058088.10/working/3D/1000 `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CC1)OCCN2C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1) `ZINC001472351939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001472351939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472351939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001472351939 none CC(C)(C)OC(=O)N1CCC2(CC1)OCCN2C(=O)[C@@]([O-])([SiH3])c1cc(Cl)cc(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 18, 29, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 3, 13, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 1, 3] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 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: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472351939 /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Finished preparing ZINC001472351939 Recording results /scratch/xiaobo/6899/xaj-8058088.10/working /scratch/xiaobo/6899/xaj-8058088.10 Appending to /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.* 0: /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472351939/0.* Removing working files in /scratch/xiaobo/6899/xaj-8058088.10/working/building/ZINC001472351939 /scratch/xiaobo/6899/xaj-8058088.10 Compressing combined databse files /scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/6899/xaj-8058088.10/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/6899/xaj-8058088.10/working/3D/1001' removed directory: `/scratch/xiaobo/6899/xaj-8058088.10/working/3D' rmdir: removing directory, `/scratch/xiaobo/6899/xaj-8058088.10/working/building' rmdir: removing directory, `/scratch/xiaobo/6899/xaj-8058088.10/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/6899/xaj-8058088.10' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaj' `/scratch/xiaobo/6899/xaj-8058088.10/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaj/finished' `/scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xaj/finished/xaj.db2.gz' removed `/scratch/xiaobo/6899/xaj-8058088.10/finished/xaj.db2.gz' removed directory: `/scratch/xiaobo/6899/xaj-8058088.10/finished' removed directory: `/scratch/xiaobo/6899/xaj-8058088.10'